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Display QPI image data #146

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Display QPI image data #146

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2b528df
enh: add simple pha and amp to gui, display not correct
Oct 24, 2023
697e125
enh: add method for qpi feature display
Oct 31, 2023
a86d100
ref: generalise the get_event method
Oct 31, 2023
0d94818
enh: correctly handle varying pha and image shapes
Nov 2, 2023
7db1900
enh: display qpi images as float and set the range via qt setView
Nov 17, 2023
44bd6c1
fix: correct the contour pixel colour based on the pixel intensity range
Nov 17, 2023
f10fc3f
enh: add quickview colormaps via pyqtgraph for phase and amp
Nov 4, 2024
ec6acc6
enh: add general dict attr for quickview that contains image show info
Nov 4, 2024
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159 changes: 116 additions & 43 deletions shapeout2/gui/quick_view/qv_main.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -133,6 +133,19 @@ def __init__(self, *args, **kwargs):
levels=(0, 255),
)

self.img_info = {
"image": {"view_event": self.imageView_image,
"view_poly": self.imageView_image_poly,
"cmap": pg.colormap.get('CET-L1')},
"qpi_pha": {"view_event": self.imageView_image_pha,
"view_poly": self.imageView_image_poly_pha,
"cmap": pg.colormap.get('CET-D1A')},
"qpi_amp": {
"view_event": self.imageView_image_amp,
"view_poly": self.imageView_image_poly_amp,
"cmap": pg.colormap.get('CET-L1')},
}

# set initial empty dataset
self._rtdc_ds = None
self.slot = None
Expand Down Expand Up @@ -201,7 +214,7 @@ def __setstate__(self, state):
self.checkBox_image_contour.setChecked(event["image contour"])
self.checkBox_image_zoom.setChecked(event["image zoom"])
self.checkBox_image_background.setChecked(
event["image background"])
event["image background"])
self.spinBox_event.setValue(event["index"])
self.checkBox_trace_raw.setChecked(event["trace raw"])
self.checkBox_trace_legend.setChecked(event["trace legend"])
Expand Down Expand Up @@ -250,28 +263,47 @@ def rtdc_ds(self, rtdc_ds):
contains_bg_feat = "image_bg" in rtdc_ds
self.checkBox_image_background.setVisible(contains_bg_feat)

def get_event_image(self, ds, event):
def get_event_image(self, ds, event, feat):
state = self.__getstate__()
imkw = self.imkw.copy()
cellimg = ds["image"][event]
# apply background correction
if "image_bg" in ds:
if state["event"]["image background"]:
bgimg = ds["image_bg"][event].astype(np.int16)
cellimg = cellimg.astype(np.int16)
cellimg = cellimg - bgimg + int(np.mean(bgimg))
# automatic contrast
if state["event"]["image auto contrast"]:
vmin, vmax = cellimg.min(), cellimg.max()
cellimg = (cellimg - vmin) / (vmax - vmin) * 255
# convert to RGB
cellimg = cellimg.reshape(
cellimg.shape[0], cellimg.shape[1], 1)
cellimg = np.repeat(cellimg, 3, axis=2)
# clip and convert to int
cellimg = np.clip(cellimg, 0, 255)
cellimg = np.require(cellimg, np.uint8, 'C')
cellimg = ds[feat][event]

if feat == "image":
# apply background correction
if "image_bg" in ds:
if state["event"]["image background"]:
bgimg = ds["image_bg"][event].astype(np.int16)
cellimg = cellimg.astype(np.int16)
cellimg = cellimg - bgimg + int(np.mean(bgimg))
# automatic contrast
if state["event"]["image auto contrast"]:
vmin, vmax = cellimg.min(), cellimg.max()
cellimg = (cellimg - vmin) / (vmax - vmin) * 255
elif "qpi" in feat:
if "qpi_pha" in feat:
imkw["levels"] = (-3, 3)
elif "qpi_amp" in feat:
imkw["levels"] = (0, 2)
else:
raise ValueError(f"Options for `feat` are 'image', "
f"'qpi_pha' and 'qpi_amp', got {feat}")

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if feat == "image":
# convert to RGB
cellimg = cellimg.reshape(
cellimg.shape[0], cellimg.shape[1], 1)
cellimg = np.repeat(cellimg, 3, axis=2)

# clip and convert to int
cellimg = np.clip(cellimg, 0, 255)
cellimg = np.require(cellimg, np.uint8, 'C')

cellimg = self.display_contour(ds, event, state, cellimg, feat, imkw)

return cellimg, imkw

@staticmethod
def display_contour(ds, event, state, cellimg, feat, imkw):
# Only load contour data if there is an image column.
# We don't know how big the images should be so we
# might run into trouble displaying random contours.
Expand All @@ -283,9 +315,18 @@ def get_event_image(self, ds, event):
# https://github.com/DC-analysis/dclab/issues/76
cont = mask ^ binary_erosion(mask)
# set red contour pixel values in original image
cellimg[cont, 0] = int(255*.7)
cellimg[cont, 1] = 0
cellimg[cont, 2] = 0
red_pix = ((imkw["levels"][1] - imkw["levels"][0])
* 0.7) - np.abs(imkw["levels"][0])
if feat == "image":
cellimg[cont, 0] = int(
red_pix) if imkw["levels"][1] == 255 else red_pix
cellimg[cont, 1] = int(imkw["levels"][0])
cellimg[cont, 2] = int(imkw["levels"][0])
else:
# just 2D images (not RGB)
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This is a work in progress (probably going to follow your idea of having specific methods for contour handling).

cellimg[cont] = int(
red_pix) if imkw["levels"][1] == 255 else red_pix

if state["event"]["image zoom"]:
xv, yv = np.where(mask)
idminx = xv.min() - 5
Expand All @@ -298,7 +339,7 @@ def get_event_image(self, ds, event):
idmaxx = idmaxx if idmaxx < shx else shx
idmaxy = idmaxy if idmaxy < shy else shy
cellimg = cellimg[idminx:idmaxx, idminy:idmaxy]
return cellimg, imkw
return cellimg

def get_statistics(self):
if self.rtdc_ds is not None:
Expand Down Expand Up @@ -334,25 +375,43 @@ def on_event_scatter_clicked(self, plot, point):
ds_idx = np.where(plotted)[0][point.index()]
self.show_event(ds_idx)

def display_img(self, feat, view, cellimg, **imkw):
self.img_info[feat][view].setImage(cellimg, **imkw)
self.img_info[feat][view].setColorMap(self.img_info[feat]["cmap"])
self.img_info[feat][view].show()

def on_event_scatter_hover(self, pos):
"""Update the image view in the polygon widget """
if self.rtdc_ds is not None and self.toolButton_poly.isChecked():
ds = self.rtdc_ds
# plotted events
plotted = self.widget_scatter.events_plotted
spos = self.widget_scatter.scatter.mapFromView(pos)
point = self.widget_scatter.scatter.pointAt(spos)
# get corrected index
event = np.where(plotted)[0][point.index()]
if "image" in self.rtdc_ds:
try:
cellimg, imkw = self.get_event_image(self.rtdc_ds, event)
except IndexError:
# the plot got updated, and we still have the old data
cellimg, imkw = self.get_event_image(self.rtdc_ds, 0)

view = "view_poly"
for key in self.img_info.keys():
self.img_info[key][view].hide()

try:
# if we have qpi data, image might be a different shape
if "qpi_pha" in ds:
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Maybe there should be a separate class entirely that handles image plotting? Generalization is not easy due to the different data types and requirements for visualization.

I think a simple method works for our use-case for image display. Could even make this into a method, seeing as we use it twice.

cellimg, imkw = self.get_event_image(ds, event, "qpi_pha")
self.display_img("qpi_pha", view, cellimg, **imkw)
if "qpi_amp" in ds:
cellimg, imkw = self.get_event_image(ds, event, "qpi_amp")
self.display_img("qpi_amp", view, cellimg, **imkw)
elif "image" in ds:
cellimg, imkw = self.get_event_image(ds, event, "image")
self.display_img("image", view, cellimg, **imkw)

except IndexError:
# the plot got updated, and we still have the old data
cellimg, imkw = self.get_event_image(self.rtdc_ds, 0, "image")
self.imageView_image_poly.setImage(cellimg, **imkw)
self.imageView_image_poly.show()
else:
self.imageView_image_poly.hide()
self.display_img("image", view, cellimg, **imkw)

def on_event_scatter_spin(self, event):
"""Sping control for event selection changed"""
Expand Down Expand Up @@ -494,8 +553,8 @@ def on_tool(self, collapse=False):
else:
# keep everything as-is but update the sizes
show_event = self.stackedWidget.currentWidget() is self.page_event
show_settings = self.stackedWidget.currentWidget() \
is self.page_settings
show_settings = (
self.stackedWidget.currentWidget() is self.page_settings)
show_poly = self.stackedWidget.currentWidget() is self.page_poly

# toolbutton checked
Expand Down Expand Up @@ -606,12 +665,25 @@ def show_event(self, event):
if self.tabWidget_event.currentIndex() == 0:
# update image
state = self.__getstate__()
if "image" in ds:
cellimg, imkw = self.get_event_image(ds, event)
self.imageView_image.setImage(cellimg, **imkw)
self.groupBox_image.show()
else:
self.groupBox_image.hide()
self.groupBox_image.hide()

view = "view_event"
for key in self.img_info.keys():
self.img_info[key][view].hide()

# if we have qpi data, image might be a different shape
if "qpi_pha" in ds:
cellimg, imkw = self.get_event_image(ds, event, "qpi_pha")
self.display_img("qpi_pha", view, cellimg, **imkw)
if "qpi_amp" in ds:
cellimg, imkw = self.get_event_image(ds, event, "qpi_amp")
self.display_img("qpi_amp", view, cellimg, **imkw)
elif "image" in ds:
cellimg, imkw = self.get_event_image(ds, event, "image")
self.display_img("image", view, cellimg, **imkw)

self.groupBox_image.show()

if "trace" in ds:
# remove legend items
for item in reversed(self.legend_trace.items):
Expand Down Expand Up @@ -650,8 +722,9 @@ def show_event(self, event):
range_t[1] = flpos + 1.5 * flwidth
range_t[2] = flmax
# set legend name
ln = "{} {}".format(self.slot.fl_name_dict[
"FL-{}".format(key[2])], key[4:])
ln = "{} {}".format(
self.slot.fl_name_dict[
"FL-{}".format(key[2])], key[4:])
self.legend_trace.addItem(self.trace_plots[key], ln)
self.legend_trace.update()
else:
Expand Down
126 changes: 108 additions & 18 deletions shapeout2/gui/quick_view/qv_main.ui
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -714,17 +714,53 @@
</layout>
</item>
<item>
<widget class="SimpleImageView" name="imageView_image">
<property name="minimumSize">
<size>
<width>300</width>
<height>100</height>
</size>
<layout class="QVBoxLayout" name="verticalLayout_11">
<property name="sizeConstraint">
<enum>QLayout::SetNoConstraint</enum>
</property>
<property name="styleSheet">
<string notr="true">background-color:transparent</string>
<property name="bottomMargin">
<number>0</number>
</property>
</widget>
<item>
<widget class="SimpleImageView" name="imageView_image">
<property name="minimumSize">
<size>
<width>300</width>
<height>100</height>
</size>
</property>
<property name="styleSheet">
<string notr="true">background-color:transparent</string>
</property>
</widget>
</item>
<item>
<widget class="SimpleImageView" name="imageView_image_pha">
<property name="minimumSize">
<size>
<width>300</width>
<height>100</height>
</size>
</property>
<property name="styleSheet">
<string notr="true">background-color:transparent</string>
</property>
</widget>
</item>
<item>
<widget class="SimpleImageView" name="imageView_image_amp">
<property name="minimumSize">
<size>
<width>300</width>
<height>100</height>
</size>
</property>
<property name="styleSheet">
<string notr="true">background-color:transparent</string>
</property>
</widget>
</item>
</layout>
</item>
</layout>
</widget>
Expand Down Expand Up @@ -1039,17 +1075,71 @@
</widget>
</item>
<item>
<widget class="SimpleImageView" name="imageView_image_poly">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
<layout class="QVBoxLayout" name="verticalLayout_15">
<property name="sizeConstraint">
<enum>QLayout::SetNoConstraint</enum>
</property>
<property name="styleSheet">
<string notr="true">opacity: 0</string>
<property name="bottomMargin">
<number>0</number>
</property>
</widget>
<item>
<widget class="SimpleImageView" name="imageView_image_poly">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>300</width>
<height>100</height>
</size>
</property>
<property name="styleSheet">
<string notr="true">opacity: 0</string>
</property>
</widget>
</item>
<item>
<widget class="SimpleImageView" name="imageView_image_poly_pha">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>300</width>
<height>100</height>
</size>
</property>
<property name="styleSheet">
<string notr="true">opacity: 0</string>
</property>
</widget>
</item>
<item>
<widget class="SimpleImageView" name="imageView_image_poly_amp">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>300</width>
<height>100</height>
</size>
</property>
<property name="styleSheet">
<string notr="true">opacity: 0</string>
</property>
</widget>
</item>
</layout>
</item>
<item>
<spacer name="verticalSpacer_3">
Expand Down