image_analysis: add grayscale option, flim: average instead of sum fo…

…r line profile

PythonGUI_apps/FLIM_analysis/FLIM_plot.py

@@ -129,7 +129,7 @@ def line_profile_update_plot(self):
 			data, coords = roi.getArrayRegion(image.view(np.ndarray), self.ui.intensity_sums_viewBox.imageItem, axes, returnMappedCoords=True)
 
 			#calculate sums along columns in region
-			sums_to_plot = np.sum(data, axis=0)
+			sums_to_plot = np.mean(data, axis=0)
 
 			#get scan x-coordinates in region
 			x_values = coords[1][0]

PythonGUI_apps/Image_analysis/Image_analysis.py

@@ -35,17 +35,18 @@ def __init__(self):
 		self.roi = self.imv.roi
 		self.roi.translateSnap = True
 		self.roi.scaleSnap = True
+		self.update_camera() #initialize camera pixel size
 		self.update_scaling_factor() #initialize scaling_factor
 
-		self.roi_plot = self.imv.getRoiPlot().getPlotItem()
-
+		self.roi_plot = self.imv.getRoiPlot().getPlotItem() #get roi plot
 		self.ui.image_groupBox.layout().addWidget(self.imv)
 
 		#set up ui signals
 		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.spot_radioButton.toggled.connect(self.update_camera)
 
 		self.num_plots = 0
 		self.show()
@@ -57,26 +58,30 @@ 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))
 
 	def resize_to_scaling_factor(self, image):
+		"""
+		Handles loading of image according to scaling_factor
+		"""
 		image = image.resize((round(image.size[0]*self.scaling_factor), round(image.size[1]*self.scaling_factor)))
-		image_array = np.asarray(image)
+		if self.ui.greyscale_checkBox.isChecked():
+			image = image.convert("L") #convert to greyscale
+		image_array = np.asarray(image).T #correct numpy array auto-flip
 		width = image_array.shape[0]
 		height = image_array.shape[1]
 		try:
-			x_vals = np.arange(width)
+			x_vals = np.arange(width) #imv x-axis
 			self.imv.setImage(img=image_array, xvals= x_vals)
 			self.roi.setPos((0,0))
 			self.roi.setSize([width, height * self.scaling_factor]) #set line roi
 			self.line_profile_update_plot()
 		except:
 			pass
 
-
 	def line_profile_update_plot(self):
 		""" Handle line profile for intensity sum viewbox """
 		self.roi_plot.clear()
@@ -118,17 +123,22 @@ def update_scaling_factor(self):
 		if self.ui.custom_pixel_size_checkBox.isChecked():
 			self.scaling_factor = self.ui.custom_pixel_size_spinBox.value()
 		else:
-			pixel_size = 7.4
-			self.scaling_factor = pixel_size/int(self.ui.magnification_comboBox.currentText())
-		self.roi.snapSize = self.scaling_factor
+			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
 		if hasattr(self, "original_image"):
-			self.resize_to_scaling_factor(self.original_image)
+			self.resize_to_scaling_factor(self.original_image) #resize image, sets up roi
 
 	def switch_custom_pixel_size(self):
 		checked = self.ui.custom_pixel_size_checkBox.isChecked()
 		self.ui.custom_pixel_size_spinBox.setEnabled(checked)
 		self.ui.magnification_comboBox.setEnabled(not checked)
 
+	def update_camera(self):
+		if self.ui.spot_radioButton.isChecked():
+			self.camera_pixel_size = 7.4
+		elif self.ui.pixera_radioButton.isChecked():
+			self.camera_pixel_size = 0
+
 	def close_application(self):
 		choice = QtGui.QMessageBox.question(self, 'EXIT!',
 											"Do you want to exit the app?",

PythonGUI_apps/Image_analysis/image_analysis_gui.ui

@@ -6,7 +6,7 @@
    <rect>
     <x>0</x>
     <y>0</y>
-    <width>1059</width>
+    <width>1029</width>
     <height>743</height>
    </rect>
   </property>
@@ -51,14 +51,21 @@
        </item>
        <item row="0" column="0">
         <layout class="QGridLayout" name="gridLayout">
-         <item row="1" column="2">
-          <widget class="QCheckBox" name="custom_pixel_size_checkBox">
+         <item row="6" column="0">
+          <widget class="QPushButton" name="load_image_pushButton">
            <property name="text">
-            <string>Custom pixel size (um)</string>
+            <string>Load image</string>
+           </property>
+          </widget>
+         </item>
+         <item row="0" column="0">
+          <widget class="QCheckBox" name="greyscale_checkBox">
+           <property name="text">
+            <string>Greyscale image</string>
            </property>
           </widget>
          </item>
-         <item row="0" column="3">
+         <item row="3" column="1">
           <widget class="QComboBox" name="magnification_comboBox">
            <item>
             <property name="text">
@@ -75,30 +82,61 @@
              <string>100</string>
             </property>
            </item>
+           <item>
+            <property name="text">
+             <string>150</string>
+            </property>
+           </item>
           </widget>
          </item>
-         <item row="1" column="3">
-          <widget class="QDoubleSpinBox" name="custom_pixel_size_spinBox">
-           <property name="enabled">
-            <bool>false</bool>
-           </property>
-          </widget>
-         </item>
-         <item row="0" column="2">
+         <item row="3" column="0">
           <widget class="QLabel" name="label_7">
            <property name="text">
             <string>Magnification</string>
            </property>
           </widget>
          </item>
-         <item row="0" column="0" colspan="2">
-          <widget class="QPushButton" name="load_image_pushButton">
+         <item row="5" column="0">
+          <widget class="QCheckBox" name="custom_pixel_size_checkBox">
            <property name="text">
-            <string>Load image</string>
+            <string>Custom pixel size (um)</string>
+           </property>
+          </widget>
+         </item>
+         <item row="5" column="1">
+          <widget class="QDoubleSpinBox" name="custom_pixel_size_spinBox">
+           <property name="enabled">
+            <bool>false</bool>
+           </property>
+          </widget>
+         </item>
+         <item row="2" column="0" colspan="2">
+          <widget class="QGroupBox" name="groupBox">
+           <property name="title">
+            <string>Camera</string>
            </property>
+           <layout class="QVBoxLayout" name="verticalLayout">
+            <item>
+             <widget class="QRadioButton" name="spot_radioButton">
+              <property name="text">
+               <string>SPOT</string>
+              </property>
+              <property name="checked">
+               <bool>true</bool>
+              </property>
+             </widget>
+            </item>
+            <item>
+             <widget class="QRadioButton" name="pixera_radioButton">
+              <property name="text">
+               <string>Pixera</string>
+              </property>
+             </widget>
+            </item>
+           </layout>
           </widget>
          </item>
-         <item row="2" column="2" colspan="2">
+         <item row="8" column="0">
           <widget class="QPushButton" name="update_scaling_factor_pushButton">
            <property name="text">
             <string>Update scaling factor</string>
@@ -117,7 +155,7 @@
     <rect>
      <x>0</x>
      <y>0</y>
-     <width>1059</width>
+     <width>1029</width>
      <height>31</height>
     </rect>
    </property>