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LAKESIDE\LindaT18
committed
initial work on image analysis
1 parent 079a67f commit 95ddb39

3 files changed

Lines changed: 269 additions & 2 deletions

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‎PythonGUI_apps/DataBrowser.py‎

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@
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from UV_Vis_analysis import uv_vis_analysis
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from PLQE_analysis import plqe_analysis
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from H5_Pkl import h5_pkl_view, h5_view_and_plot
21-
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from Image_analysis import Image_analysis
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pg.mkQApp()
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#pg.setConfigOption('background', 'w')
2424

@@ -38,7 +38,7 @@ def __init__(self):
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self.ui = WindowTemplate()
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self.ui.setupUi(self)
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self.ui.select_comboBox.addItems(["Lifetime Analysis", "Spectrum Analysis", "FLIM Analysis",
41-
"UV-Vis Analysis", "PLQE Analysis", "H5 View/Plot", "H5/PKL Viewer"])
41+
"UV-Vis Analysis", "PLQE Analysis", "H5 View/Plot", "H5/PKL Viewer", "Image Analysis"])
4242
self.ui.load_pushButton.clicked.connect(self.load_app)
4343

4444
self.show()
@@ -69,6 +69,9 @@ def load_app(self):
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elif analysis_software == "H5/PKL Viewer":
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app = h5_pkl_view.H5PklView(sys.argv)
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#sys.exit(app.exec_())
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elif analysis_software == "Image Analysis":
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self.image_window = Image_analysis.MainWindow()
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self.image_window.show()
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‎PythonGUI_apps/Image_analysis/Image_analysis.py‎

Lines changed: 142 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,142 @@
1+
import sys
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from pathlib import Path
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import os.path
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import pyqtgraph as pg
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from pyqtgraph.Qt import QtCore, QtGui, QtWidgets#, QColorDialog
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import numpy as np
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import matplotlib.pyplot as plt
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from PIL import Image
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# local modules
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pg.mkQApp()
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base_path = Path(__file__).parent
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file_path = (base_path / "image_analysis_gui.ui").resolve()
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17+
uiFile = file_path
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WindowTemplate, TemplateBaseClass = pg.Qt.loadUiType(uiFile)
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class MainWindow(TemplateBaseClass):
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def __init__(self):
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super(TemplateBaseClass, self).__init__()
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# Create the main window
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self.ui = WindowTemplate()
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self.ui.setupUi(self)
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#setup imageview
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self.imv = pg.ImageView()
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self.imv.getView().setAspectLocked(lock=False, ratio=1)
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self.imv.getView().setMouseEnabled(x=True, y=True)
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self.imv.getView().invertY(False)
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self.roi = self.imv.roi
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self.roi.translateSnap = True
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self.roi.scaleSnap = True
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self.calc_scaling_factor() #initialize scaling_factor
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self.roi.snapSize = self.scaling_factor #roi snaps to multiples of scaling_factor
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self.roi.sigRegionChanged.connect(self.line_profile_update_plot)
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self.roi_plot = self.imv.getRoiPlot().getPlotItem()
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self.ui.image_groupBox.layout().addWidget(self.imv)
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#set up ui signals
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self.ui.load_image_pushButton.clicked.connect(self.load_image)
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self.ui.custom_pixel_size_checkBox.stateChanged.connect(self.switch_custom_pixel_size)
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self.show()
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def load_image(self):
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"""
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Prompts the user to select a text file containing image data.
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"""
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try:
56+
file = QtWidgets.QFileDialog.getOpenFileName(self, 'Open file', os.getcwd())
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image = Image.open(file[0])
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image = image.rotate(-90, expand=True)
59+
image_array = np.asarray(image)
60+
try:
61+
width = image_array.shape[0]
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height = image_array.shape[1]
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x_vals = np.arange(width)
64+
self.imv.setImage(img=image_array, xvals= x_vals)
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self.calc_scaling_factor()
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self.roi.setPos((0,0))
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self.roi.setSize([width, height*self.scaling_factor]) #set line roi
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self.line_profile_update_plot()
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except:
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pass
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except Exception as err:
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print(format(err))
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74+
def line_profile_update_plot(self):
75+
""" Handle line profile for intensity sum viewbox """
76+
#if hasattr(self, "intensity_sums"):
77+
self.roi_plot.clear()
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image = self.imv.getProcessedImage()
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# Extract image data from ROI
82+
axes = (self.imv.axes['x'], self.imv.axes['y'])
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data, coords = self.roi.getArrayRegion(image.view(np.ndarray), self.imv.imageItem, axes, returnMappedCoords=True)
84+
if data is None:
85+
return
86+
87+
self.calc_scaling_factor()
88+
x_values = coords[1][0] * self.scaling_factor #adjust x-axis roi plot
89+
90+
#calculate sums along columns in region
91+
if len(data.shape) == 2: #if grayscale, average intensities
92+
sums_to_plot = np.mean(data, axis=0)
93+
try:
94+
self.roi_plot.plot(x_values, sums_to_plot)
95+
except:
96+
pass
97+
elif len(data.shape) > 2: #if rgb arrays, plot individual components
98+
r_values = data[:,:,0]
99+
g_values = data[:,:,1]
100+
b_values = data[:,:,2]
101+
r_avg = np.mean(r_values, axis=0) #average red values across columns
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g_avg = np.mean(g_values, axis=0) #average green values
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b_avg = np.mean(b_values, axis=0) #average blue values
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try:
105+
self.roi_plot.plot(x_values, r_avg, pen='r')
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self.roi_plot.plot(x_values, g_avg, pen='g')
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self.roi_plot.plot(x_values, b_avg, pen='b')
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except:
109+
pass
110+
111+
def calc_scaling_factor(self):
112+
"""
113+
Calculate scaling factor
114+
"""
115+
if self.ui.custom_pixel_size_checkBox.isChecked():
116+
self.scaling_factor = self.ui.custom_pixel_size_spinBox.value()
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else:
118+
pixel_size = 7.4
119+
self.scaling_factor = pixel_size/int(self.ui.magnification_comboBox.currentText())
120+
121+
def switch_custom_pixel_size(self):
122+
checked = self.ui.custom_pixel_size_checkBox.isChecked()
123+
self.ui.custom_pixel_size_spinBox.setEnabled(checked)
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self.ui.magnification_comboBox.setEnabled(not checked)
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126+
def close_application(self):
127+
choice = QtGui.QMessageBox.question(self, 'EXIT!',
128+
"Do you want to exit the app?",
129+
QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
130+
if choice == QtGui.QMessageBox.Yes:
131+
sys.exit()
132+
else:
133+
pass
134+
135+
"""Run the Main Window"""
136+
def run():
137+
win = MainWindow()
138+
QtGui.QApplication.instance().exec_()
139+
return win
140+
141+
#Uncomment below if you want to run this as standalone
142+
#run()

‎PythonGUI_apps/Image_analysis/image_analysis_gui.ui‎

Lines changed: 122 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,122 @@
1+
<?xml version="1.0" encoding="UTF-8"?>
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<ui version="4.0">
3+
<class>MainWindow</class>
4+
<widget class="QMainWindow" name="MainWindow">
5+
<property name="geometry">
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<rect>
7+
<x>0</x>
8+
<y>0</y>
9+
<width>1050</width>
10+
<height>743</height>
11+
</rect>
12+
</property>
13+
<property name="windowTitle">
14+
<string>MainWindow</string>
15+
</property>
16+
<property name="tabShape">
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<enum>QTabWidget::Triangular</enum>
18+
</property>
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<widget class="QWidget" name="centralwidget">
20+
<layout class="QGridLayout" name="gridLayout_2">
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<item row="0" column="0">
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<widget class="QGroupBox" name="image_groupBox">
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<property name="sizePolicy">
24+
<sizepolicy hsizetype="Expanding" vsizetype="Preferred">
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<horstretch>0</horstretch>
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<verstretch>0</verstretch>
27+
</sizepolicy>
28+
</property>
29+
<property name="minimumSize">
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<size>
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<width>600</width>
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<height>0</height>
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</size>
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</property>
35+
<property name="title">
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<string>Image</string>
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</property>
38+
<layout class="QGridLayout" name="gridLayout_3"/>
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</widget>
40+
</item>
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<item row="0" column="1">
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<widget class="QGroupBox" name="groupBox_2">
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<property name="title">
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<string>Settings</string>
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</property>
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<layout class="QGridLayout" name="gridLayout_4">
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<item row="2" column="0">
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<widget class="QWidget" name="line_profile_placeholder" native="true">
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<layout class="QGridLayout" name="gridLayout_7"/>
50+
</widget>
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</item>
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<item row="0" column="0">
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<layout class="QGridLayout" name="gridLayout">
54+
<item row="0" column="0" colspan="2">
55+
<widget class="QPushButton" name="load_image_pushButton">
56+
<property name="text">
57+
<string>Load image</string>
58+
</property>
59+
</widget>
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</item>
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<item row="0" column="3">
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<widget class="QComboBox" name="magnification_comboBox">
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<item>
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<property name="text">
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<string>50</string>
66+
</property>
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</item>
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<item>
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<property name="text">
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<string>75</string>
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</property>
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</item>
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<item>
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<property name="text">
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<string>100</string>
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</property>
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</item>
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</widget>
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</item>
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<item row="0" column="2">
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<widget class="QLabel" name="label_7">
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<property name="text">
83+
<string>Magnification</string>
84+
</property>
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</widget>
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</item>
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<item row="1" column="2">
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<widget class="QCheckBox" name="custom_pixel_size_checkBox">
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<property name="text">
90+
<string>Custom pixel size (um)</string>
91+
</property>
92+
</widget>
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</item>
94+
<item row="1" column="3">
95+
<widget class="QDoubleSpinBox" name="custom_pixel_size_spinBox">
96+
<property name="enabled">
97+
<bool>false</bool>
98+
</property>
99+
</widget>
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</item>
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</layout>
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</item>
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</layout>
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</widget>
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</item>
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</layout>
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</widget>
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<widget class="QMenuBar" name="menubar">
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<property name="geometry">
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<rect>
111+
<x>0</x>
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<y>0</y>
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<width>1050</width>
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<height>31</height>
115+
</rect>
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</property>
117+
</widget>
118+
<widget class="QStatusBar" name="statusbar"/>
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</widget>
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<resources/>
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<connections/>
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</ui>

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