Added manual segmentation tool to SegUI

Added a new tab to SegUI to enable manual segmentation of images.

The manual segmentation is saved as manual_mask.npy in the parameters directory. This is then automatically loaded if 'UI' is passed as the mask argument in ParticleAnalysis.

To manually segment, users left-click and drag around the border of a particle. They then right-click within the red border. Note: do not right-click if the border is incomplete!

Author: TomSlater

ParticleSpy/Parameters/manual_mask.npy

@@ -57,7 +57,9 @@ def ParticleAnalysis(acquisition,parameters,particles=None,mask=np.zeros((1))):
         image = acquisition
         ac_types = 'Image only'
 
-    if mask.sum()==0:
+    if mask == 'UI':
+        labeled = label(np.load(inspect.getfile(process).rpartition('\\')[0]+'/Parameters/manual_mask.npy'))
+    elif mask.sum()==0:
         labeled = process(image,parameters)
         #labels = np.unique(labeled).tolist() #some labeled number have been removed by "remove_small_holes" function
     else:

ParticleSpy/ParticleAnalysis.py

@@ -6,15 +6,18 @@
 """
 
 from PyQt5.QtWidgets import QCheckBox, QPushButton, QLabel, QMainWindow, QSpinBox
-from PyQt5.QtWidgets import QApplication, QWidget, QVBoxLayout, QComboBox, QTabWidget
-from PyQt5.QtGui import QPixmap, QImage
+from PyQt5.QtWidgets import QApplication, QWidget, QHBoxLayout, QComboBox, QTabWidget
+from PyQt5.QtWidgets import QVBoxLayout
+from PyQt5.QtGui import QPixmap, QImage, QColor, QPainter, QBitmap
 from PyQt5.QtCore import Qt
 import sys
 
 import inspect
 import numpy as np
-from skimage.segmentation import mark_boundaries
+from skimage.segmentation import mark_boundaries, flood_fill
 from skimage.util import invert
+import matplotlib.pyplot as plt
+from PIL import Image
 
 from ParticleSpy.segptcls import process
 from ParticleSpy.ParticleAnalysis import parameters
@@ -34,7 +37,7 @@ def __init__(self,im_hs):
 
         offset = 50
 
-        self.layout = QVBoxLayout(self)
+        self.layout = QHBoxLayout(self)
 
         # Initialize tab screen
         self.tabs = QTabWidget()
@@ -47,45 +50,41 @@ def __init__(self,im_hs):
 
         #self.central_widget = QWidget()               
         #self.setCentralWidget(self.central_widget)
-        lay = QVBoxLayout()
+        lay = QHBoxLayout()
+        leftlay = QVBoxLayout()
+        rightlay = QVBoxLayout()
         self.tab1.setLayout(lay)
 
         self.label = QLabel(self)
         qi = QImage(self.image.data, self.image.shape[1], self.image.shape[0], self.image.shape[1], QImage.Format_Grayscale8)
         pixmap = QPixmap(qi)
-        pixmap2 = pixmap.scaled(512, 512, Qt.KeepAspectRatio)
-        self.label.setPixmap(pixmap2)
-        self.label.setGeometry(10,10,pixmap2.width(),pixmap2.height())
+        self.pixmap2 = pixmap.scaled(512, 512, Qt.KeepAspectRatio)
+        self.label.setPixmap(self.pixmap2)
+        self.label.setGeometry(10,10,self.pixmap2.width(),self.pixmap2.height())
 
-        height = max((pixmap2.height()+50,300 + offset)) #300 +50
+        height = max((self.pixmap2.height()+50,300 + offset)) #300 +50
 
-        self.resize(pixmap2.width()+130, height)
+        self.resize(self.pixmap2.width()+130, height)
 
         self.filt_title = QLabel(self)
         self.filt_title.setText('Pre-filtering options')
-        self.filt_title.move(pixmap2.width()+20, 0)
 
         self.sptxt = QLabel(self)
         self.sptxt.setText('Rolling ball size')
-        self.sptxt.move(pixmap2.width()+20,20)
 
         self.sp = QSpinBox(self)
         self.sp.setMaximum(self.image.shape[0])
         self.sp.valueChanged.connect(self.rollingball)
-        self.sp.move(pixmap2.width()+20, 45)
 
         self.gausstxt = QLabel(self)
         self.gausstxt.setText('Gaussian filter kernel size')
-        self.gausstxt.move(pixmap2.width()+20,70)
 
         self.gauss = QSpinBox(self)
         self.gauss.setMaximum(self.image.shape[0])
         self.gauss.valueChanged.connect(self.gaussian)
-        self.gauss.move(pixmap2.width()+20, 95)
 
         self.thresh_title = QLabel(self)
         self.thresh_title.setText('Thresholding options')
-        self.thresh_title.move(pixmap2.width()+20, 135)
 
         self.comboBox = QComboBox(self)
         self.comboBox.addItem("Otsu")
@@ -97,72 +96,90 @@ def __init__(self,im_hs):
         self.comboBox.addItem("Local")
         self.comboBox.addItem("Local Otsu")
         self.comboBox.addItem("Local+Global Otsu")
-        self.comboBox.move(pixmap2.width()+20, 160)
         self.comboBox.activated[str].connect(self.threshold_choice)
 
         self.localtxt = QLabel(self)
         self.localtxt.setText('Local filter kernel')
-        self.localtxt.move(pixmap2.width()+20,195)
 
         self.local_size = QSpinBox(self)
         self.local_size.setMaximum(self.image.shape[0])
         self.local_size.valueChanged.connect(self.local)
-        self.local_size.move(pixmap2.width()+20, 220)
 
         cb = QCheckBox('Watershed', self)
-        cb.move(pixmap2.width()+20, 260)
         cb.stateChanged.connect(self.changeWatershed)
 
         cb2 = QCheckBox('Invert', self)
-        cb2.move(pixmap2.width()+20, 260 + offset /2 )
         cb2.stateChanged.connect(self.changeInvert)
 
         self.minsizetxt = QLabel(self)
         self.minsizetxt.setText('Min particle size (px)')
-        self.minsizetxt.move(pixmap2.width()+20, 280+offset)
 
         self.minsizev = QSpinBox(self)
         self.minsizev.setMaximum(self.image.shape[0]*self.image.shape[1])
         self.minsizev.valueChanged.connect(self.minsize)
-        self.minsizev.move(pixmap2.width()+20, 305+offset)
 
         updateb = QPushButton('Update',self)
-        updateb.move(pixmap2.width()+20,355+offset)
         updateb.clicked.connect(self.update)
 
         paramsb = QPushButton('Get Params',self)
-        paramsb.move(pixmap2.width()+20,385+offset)
 
         paramsb.clicked.connect(self.return_params)
 
         self.imagetxt = QLabel(self)
         self.imagetxt.setText('Display:')
-        self.imagetxt.move(75, pixmap2.height()+15)
 
         self.imBox = QComboBox(self)
         self.imBox.addItem("Image")
         self.imBox.addItem("Labels")
-        self.imBox.move(pixmap2.width()/2-10, pixmap2.height()+15)
 
         self.imBox.activated[str].connect(self.changeIm)
-        
-        lay.addWidget(self.thresh_title)
-        lay.addWidget(self.filt_title)
-        lay.addWidget(self.label)
-        lay.addWidget(self.comboBox)
-        lay.addWidget(self.sp)
-        lay.addWidget(self.sptxt)
-        lay.addWidget(self.gauss)
-        lay.addWidget(self.gausstxt)
-        lay.addWidget(self.imagetxt)
-        lay.addWidget(self.minsizev)
-        
+
+        leftlay.addWidget(self.label)
+        leftlay.addWidget(self.imagetxt)
+        leftlay.addWidget(self.imBox)
+
+        rightlay.addWidget(self.filt_title) 
+        rightlay.addWidget(self.sptxt)
+        rightlay.addWidget(self.sp)
+        rightlay.addWidget(self.gausstxt)
+        rightlay.addWidget(self.gauss)
+        rightlay.addStretch(1)
+        rightlay.addWidget(self.thresh_title)
+        rightlay.addWidget(self.comboBox)
+        rightlay.addStretch(1)
+        rightlay.addWidget(self.localtxt)
+        rightlay.addWidget(self.local_size)
+        rightlay.addStretch(1)
+        rightlay.addWidget(cb)
+        rightlay.addWidget(cb2)
+        rightlay.addStretch(1)
+        rightlay.addWidget(self.minsizetxt)
+        rightlay.addWidget(self.minsizev)
+        rightlay.addStretch(2)
+        rightlay.addWidget(updateb)
+        rightlay.addWidget(paramsb)
+        
+        lay.addLayout(leftlay)
+        lay.addLayout(rightlay)
 
         self.layout.addWidget(self.tabs)
         self.setLayout(self.layout)
 
         self.setCentralWidget(self.tabs)
 
+        #Tab 2
+        self.canvas = Canvas(self.pixmap2)
+        #self.canvas = Drawer(self.pixmap2)
+        
+        self.getarrayb = QPushButton('Save Segmentation',self)
+        self.getarrayb.clicked.connect(self.save_array)
+        
+        tab2layout = QVBoxLayout()
+        tab2layout.addWidget(self.canvas)
+        tab2layout.addWidget(self.getarrayb)
+        tab2layout.addStretch(1)
+        self.tab2.setLayout(tab2layout)
+        
         self.show()
 
     def getim(self,im_hs):
@@ -198,8 +215,8 @@ def changeInvert(self, state):
             qi = QImage(self.image.data, self.image.shape[1], self.image.shape[0], self.image.shape[1], QImage.Format_Indexed8)
 
         pixmap = QPixmap(qi)
-        pixmap2 = pixmap.scaled(512, 512, Qt.KeepAspectRatio)
-        self.label.setPixmap(pixmap2)
+        self.pixmap2 = pixmap.scaled(512, 512, Qt.KeepAspectRatio)
+        self.label.setPixmap(self.pixmap2)
 
     def rollingball(self):
         if self.sp.value() == 1:
@@ -273,7 +290,78 @@ def threshold_choice(self):
             self.params.segment['threshold'] = "local_otsu"
         if str(self.comboBox.currentText()) == "Local+Global Otsu":
             self.params.segment['threshold'] = "lg_otsu"
+            
+    def save_array(self):
+        self.canvas.savearray(self.image)
+
+
+class Canvas(QLabel):
+
+    def __init__(self,pixmap):
+        super().__init__()
+        self.setPixmap(pixmap)
+
+        self.last_x, self.last_y = None, None
+        self.pen_color = QColor(255, 0, 0, 20)        
+
+    def set_pen_color(self, c):
+        self.pen_color = QColor(c)
+        
+    def mousePressEvent(self, e):
+        if e.button() == Qt.RightButton:
+            image = self.pixmap().toImage()
+            b = image.bits()
+            b.setsize(512 * 512 * 4)
+            arr = np.frombuffer(b, np.uint8).reshape((512, 512, 4))
+            
+            arr_test = arr[:,:,0]/arr[:,:,2]
+            
+            painted_arr = np.zeros_like(arr[:,:,0:3])
+            painted_arr[:,:,2][arr_test!=1] = 255
+            
+            painted_arr[:,:,2] = flood_fill(painted_arr[:,:,2],(e.y(),e.x()),255)
+            
+            qi = QImage(painted_arr.data, painted_arr.shape[1], painted_arr.shape[0], 3*painted_arr.shape[1], QImage.Format_RGB888)
+            pixmap = QPixmap(qi)
+            
+            painter = QPainter(self.pixmap())
+            painter.setOpacity(0.01)
+
+            painter.drawPixmap(0, 0, pixmap)
+            painter.end()
+            self.update()
+            
+            self.array = painted_arr[:,:,2]
+
+    def mouseMoveEvent(self, e):
+        if e.buttons() == Qt.LeftButton:
+            if self.last_x is None: # First event.
+                self.last_x = e.x()
+                self.last_y = e.y()
+                return # Ignore the first time.
+            
+            painter = QPainter(self.pixmap())
+            p = painter.pen()
+            p.setWidth(4)
+            p.setColor(self.pen_color)
+            painter.setPen(p)
+            painter.drawLine(self.last_x, self.last_y, e.x(), e.y())
+            painter.end()
+            self.update()
 
+            # Update the origin for next time.
+            self.last_x = e.x()
+            self.last_y = e.y()
+
+    def mouseReleaseEvent(self, e):
+        self.last_x = None
+        self.last_y = None
+        
+    def savearray(self,image):
+        resized = np.array(Image.fromarray(self.array).resize((image.shape[0],image.shape[1])))
+        np.save('Parameters/manual_mask',resized)
+
+
 def main(haadf):
 
     ex = Application(haadf)
@@ -299,6 +387,9 @@ def SegUI(image):
     import hyperspy.api as hs
     filename = "Data/JEOL HAADF Image.dm4"
     haadf = hs.load(filename)
+    
+    image_out = np.zeros_like(haadf)
+    
     app = QApplication(sys.argv)
     app.aboutToQuit.connect(app.deleteLater)
 

ParticleSpy/SegUI.py

@@ -3,7 +3,8 @@
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
-install_requires=["hyperspy"]
+install_requires=["hyperspy",
+                  "scikit-image>=0.15"]
 
 try:
     import PyQt5  # noqa