image analysis: fix image orientation, roi height, add scalebar; spectra analysis: fix scalebar

Author: LAKESIDE\LindaT18

PythonGUI_apps/FLIM_analysis/FLIM_plot.py

@@ -112,7 +112,7 @@ def plot_intensity_sums(self):
                                                   (self.x_step_size,
                                                    self.y_step_size))
             self.ui.intensity_sums_viewBox.roi.setSize([self.x_scan_size, self.y_step_size]) #line roi
-            scale = pg.ScaleBar(size=3,suffix='um')
+            scale = pg.ScaleBar(size=1,suffix='um')
             scale.setParentItem(self.ui.intensity_sums_viewBox.view)
             scale.anchor((1, 1), (1, 1), offset=(-30, -30))
             self.ui.intensity_sums_viewBox.view.sigRangeChanged.connect(lambda: updateDelay(scale, 10))

PythonGUI_apps/Image_analysis/Image_analysis.py

@@ -10,6 +10,7 @@
 # local modules
 
 pg.mkQApp()
+pg.setConfigOption('imageAxisOrder', 'col-major') 
 
 base_path = Path(__file__).parent
 file_path = (base_path / "image_analysis_gui.ui").resolve()
@@ -18,6 +19,10 @@
 
 WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile)
 
+def updateDelay(scale, time):
+	""" Hack fix for scalebar inaccuracy"""
+	QtCore.QTimer.singleShot(time, scale.updateBar)
+
 class MainWindow(TemplateBaseClass):  
 
 	def __init__(self):
@@ -45,10 +50,9 @@ def __init__(self):
 		self.roi.sigRegionChanged.connect(self.line_profile_update_plot)
 		self.ui.load_image_pushButton.clicked.connect(self.load_image)
 		self.ui.custom_pixel_size_checkBox.stateChanged.connect(self.switch_custom_pixel_size)
-		self.ui.update_scaling_factor_pushButton.clicked.connect(self.update_scaling_factor)
+		self.ui.update_scaling_factor_pushButton.clicked.connect(self.reload_image)
 		self.ui.spot_radioButton.toggled.connect(self.update_camera)
 
-		self.num_plots = 0
 		self.show()
 
 	def load_image(self):
@@ -58,7 +62,7 @@ def load_image(self):
 		try:
 			file = QtWidgets.QFileDialog.getOpenFileName(self, 'Open file', os.getcwd())
 			self.original_image = Image.open(file[0])
-			#self.original_image = self.original_image.rotate(-90, expand=True)
+			self.original_image = self.original_image.rotate(-90, expand=True)
 			self.resize_to_scaling_factor(self.original_image)
 		except Exception as err:
 			print(format(err))
@@ -67,17 +71,25 @@ def resize_to_scaling_factor(self, image):
 		"""
 		Handles loading of image according to scaling_factor
 		"""
+		self.update_camera() #initialize camera pixel size
+		self.update_scaling_factor() #initialize scaling_factor
 		image = image.resize((round(image.size[0]*self.scaling_factor), round(image.size[1]*self.scaling_factor)))
 		if self.ui.greyscale_checkBox.isChecked():
 			image = image.convert("L") #convert to greyscale
-		image_array = np.asarray(image).T #correct numpy array auto-flip
+		image_array = np.array(image) #correct numpy array auto-flip
+
 		width = image_array.shape[0]
 		height = image_array.shape[1]
 		try:
 			x_vals = np.arange(width) #imv x-axis
-			self.imv.setImage(img=image_array, xvals= x_vals)
+			self.imv.setImage(image_array, xvals= x_vals)
 			self.roi.setPos((0,0))
-			self.roi.setSize([width, height * self.scaling_factor]) #set line roi
+			self.roi.setSize([width, self.camera_pixel_size])
+
+			scale = pg.ScaleBar(size=1,suffix='um')
+			scale.setParentItem(self.imv.view)
+			scale.anchor((1, 1), (1, 1), offset=(-30, -30))
+			self.imv.view.sigRangeChanged.connect(lambda: updateDelay(scale, 10))
 			self.line_profile_update_plot()
 		except:
 			pass
@@ -121,10 +133,13 @@ def update_scaling_factor(self):
 		Calculate scaling factor
 		"""
 		if self.ui.custom_pixel_size_checkBox.isChecked():
-			self.scaling_factor = self.ui.custom_pixel_size_spinBox.value()
+			self.camera_pixel_size = self.ui.custom_pixel_size_spinBox.value()
+			self.scaling_factor = self.camera_pixel_size
 		else:
 			self.scaling_factor = self.camera_pixel_size/int(self.ui.magnification_comboBox.currentText())
 		self.roi.snapSize = self.scaling_factor #roi snaps to multiples of scaling_factor
+
+	def reload_image(self):
 		if hasattr(self, "original_image"):
 			self.resize_to_scaling_factor(self.original_image) #resize image, sets up roi
 

PythonGUI_apps/Image_analysis/image_analysis_gui.ui

@@ -11,7 +11,7 @@
    </rect>
   </property>
   <property name="windowTitle">
-   <string>MainWindow</string>
+   <string>Image Analysis</string>
   </property>
   <property name="tabShape">
    <enum>QTabWidget::Triangular</enum>

PythonGUI_apps/Spectrum_analysis/Spectra_plot_fit.py

@@ -44,6 +44,10 @@
 
 WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile)
 
+def updateDelay(scale, time):
+	""" Hack fix for scalebar inaccuracy"""
+	QtCore.QTimer.singleShot(time, scale.updateBar)
+
 class MainWindow(TemplateBaseClass):  
 
 	def __init__(self):
@@ -539,11 +543,12 @@ def plot_fit_scan(self):
 				scale = pg.ScaleBar(size=2,suffix='um')
 				scale.setParentItem(self.ui.fit_scan_viewbox.view)
 				scale.anchor((1, 1), (1, 1), offset=(-30, -30))
+				self.ui.fit_scan_viewbox.view.sigRangeChanged.connect(lambda: updateDelay(scale, 10))
 			else:
 				self.ui.fit_scan_viewbox.setImage(self.img)
 
 			self.ui.fit_scan_viewbox.view.invertY(False)
-				
+
 		except Exception as e:
 			self.ui.result_textBrowser2.append(str(e))
 			pass
@@ -553,20 +558,18 @@ def plot_raw_scan(self):
 			# TODO test line scan plots
 
 			intensities = self.intensities.T #this is only there because of how we are saving the data in the app
-			
-			intensities = np.reshape(intensities, newshape=(2048,self.numb_x_pixels, self.numb_y_pixels))
-			
-			self.ui.raw_scan_viewbox.view.invertY(False)
+			intensities = np.reshape(intensities, newshape=(2048,self.numb_x_pixels, self.numb_y_pixels)) 
 			self.ui.raw_scan_viewbox.setImage(intensities, scale=
 												  (self.x_step_size,
 												   self.y_step_size), xvals=self.wavelengths)
 
-
 			#roi_plot = self.ui.raw_scan_viewBox.getRoiPlot()
 			#roi_plot.plot(data['Wavelengths'], intensities)
+			self.ui.raw_scan_viewbox.view.invertY(False)
 			scale = pg.ScaleBar(size=2,suffix='um')
 			scale.setParentItem(self.ui.raw_scan_viewbox.view)
 			scale.anchor((1, 1), (1, 1), offset=(-30, -30))
+			self.ui.raw_scan_viewbox.view.sigRangeChanged.connect(lambda: updateDelay(scale, 10))
 
 		except Exception as e:
 			self.ui.result_textBrowser2.append(str(e))
@@ -588,6 +591,7 @@ def plot_intensity_sums(self):
 			scale = pg.ScaleBar(size=2,suffix='um')
 			scale.setParentItem(self.ui.intensity_sums_viewBox.view)
 			scale.anchor((1, 1), (1, 1), offset=(-30, -30))
+			self.ui.intensity_sums_viewbox.view.sigRangeChanged.connect(lambda: updateDelay(scale, 10))
 
 		except Exception as e:
 			self.ui.result_textBrowser2.append(str(e))