added DBSCAN clusters to autodraw on plot

Author: carsen-stringer

rastermap/gui.py

@@ -8,9 +8,10 @@
 from pyqtgraph import GraphicsScene
 from scipy.stats import zscore
 from matplotlib import cm
-from rastermap.roi import gROI
+from rastermap.roi import gROI, dbROI
 import rastermap.run
 from rastermap import Rastermap
+from sklearn.cluster import DBSCAN
 
 def triangle_area(p):
     area = 0.5 * np.abs(p[0,0] * p[1,1] - p[0,0] * p[2,1] +
@@ -231,7 +232,7 @@ def __init__(self):
         self.makegrid.clicked.connect(self.make_grid)
         self.makegrid.setStyleSheet(self.styleInactive)
         self.makegrid.setEnabled(False)
-        self.makegrid.setFixedWidth(100)
+        self.makegrid.setFixedWidth(200)
         self.l0.addWidget(self.makegrid, rs+7, 0, 1, 1)
         self.gridsize = QtGui.QLineEdit(self)
         self.gridsize.setValidator(QtGui.QIntValidator(2, 20))
@@ -241,6 +242,21 @@ def __init__(self):
         self.gridsize.returnPressed.connect(self.make_grid)
         self.l0.addWidget(self.gridsize, rs+7, 1, 1, 1)
 
+        self.dbbutton = QtGui.QPushButton("DBSCAN clusters, ms=")
+        self.dbbutton.setFont(QtGui.QFont("Arial", 8, QtGui.QFont.Bold))
+        self.dbbutton.clicked.connect(self.dbscan)
+        self.dbbutton.setStyleSheet(self.styleInactive)
+        self.dbbutton.setEnabled(False)
+        self.dbbutton.setFixedWidth(200)
+        self.l0.addWidget(self.dbbutton, rs+8, 0, 1, 1)
+        self.min_samples = QtGui.QLineEdit(self)
+        self.min_samples.setValidator(QtGui.QIntValidator(5, 200))
+        self.min_samples.setText("50")
+        self.min_samples.setFixedWidth(45)
+        self.min_samples.setAlignment(QtCore.Qt.AlignRight)
+        self.min_samples.returnPressed.connect(self.dbscan)
+        self.l0.addWidget(self.min_samples, rs+8, 1, 1, 1)
+
         ysm = QtGui.QLabel("<font color='white'>y-binning</font>")
         ysm.setFixedWidth(100)
         self.l0.addWidget(ysm, rs+6, 0, 1, 1)
@@ -295,11 +311,13 @@ def __init__(self):
         # self.load_behavior('C:/Users/carse/github/TX4/beh.npy')
         self.file_iscell = None
         #self.fname = '/media/carsen/DATA2/grive/rastermap/DATA/embedding.npy'
-        #self.load_proc(self.fname)
+        self.fname = 'D:/grive/cshl_suite2p/TX39/embedding.npy'
+        self.load_proc(self.fname)
 
         self.show()
         self.win.show()
 
+
     def add_imgROI(self):
         if hasattr(self, 'imgROI'):
             self.pfull.removeItem(self.imgROI)
@@ -509,6 +527,22 @@ def update_selected(self, ineur):
             ineur = self.selected[ineur]
             self.xp.setData(pos=self.embedding[ineur,:][np.newaxis,:])
 
+    def dbscan(self):
+        ms = int(self.min_samples.text())
+        # remove previous ROIs
+        if len(self.ROIs) > 0:
+            for n in range(len(self.ROIs)):
+                self.ROI_delete()
+
+        db = DBSCAN(eps=0.8, min_samples=ms).fit(self.embedding)
+        ilabels = np.unique(db.labels_)
+        ilabels = ilabels[ilabels>=0]
+        print(ilabels)
+        #ilabels = ilabels[:1]
+        for i in ilabels:
+            self.dbROI_add((db.labels_==i).nonzero()[0])
+        self.ROI_selection()
+
     def make_grid(self):
         ng = int(self.gridsize.text())
         if len(self.ROIs) > 0:
@@ -531,6 +565,15 @@ def make_grid(self):
                 self.ROI_add(pos, prect, color=jet[j+k*ng]*255.0)
         self.ROI_selection()
 
+    def dbROI_add(self, selected, color=None):
+        if color is None:
+            color =  np.random.randint(255,size=(3,))
+        self.ROIs.append(dbROI(selected, color, self))
+        self.Rselected.append(self.ROIs[-1].selected)
+        self.Rcolors.append(np.reshape(np.tile(self.ROIs[-1].color, 10 * self.Rselected[-1].size),
+                            (self.Rselected[-1].size, 10, 3)))
+        self.ROIorder.append(len(self.ROIs)-1)
+
     def ROI_add(self, pos, prect, color=None):
         if color is None:
             color =  np.random.randint(255,size=(3,))
@@ -586,9 +629,12 @@ def enable_embedded(self):
         self.updateROI.setEnabled(True)
         self.saveROI.setEnabled(True)
         self.makegrid.setEnabled(True)
+        self.dbbutton.setEnabled(True)
+
         self.updateROI.setStyleSheet(self.styleUnpressed)
         self.saveROI.setStyleSheet(self.styleUnpressed)
         self.makegrid.setStyleSheet(self.styleUnpressed)
+        self.dbbutton.setStyleSheet(self.styleUnpressed)
 
     def disable_embedded(self):
         self.updateROI.setEnabled(False)
@@ -649,8 +695,6 @@ def mouse_moved_bar(self, pos):
                 ineur = min(self.colormat.shape[0]-1, max(0, int(np.floor(y))))
                 self.update_selected(ineur)
 
-
-
     def plot_clicked(self, event):
         """left-click chooses a cell, right-click flips cell to other view"""
         flip = False

rastermap/roi.py

@@ -11,6 +11,34 @@ def triangle_area(p0, p1, p2):
            p2[:,0] * p0[1] - p2[:,0] * p1[1])
     return area
 
+class dbROI():
+    """
+    ROI that is premade from DBSCAN clustering
+    """
+    def __init__(self, selected, color, parent=None):
+        self.color = color
+        self.selected = selected
+        self.positions = parent.embedding[self.selected, :]
+        self.pen = pg.mkPen(pg.mkColor(self.color),
+                                width=1,
+                                style=QtCore.Qt.SolidLine)
+        self.ROIplot = pg.ScatterPlotItem(pos=self.positions, pen=self.pen, symbol='o', size=2)
+        parent.p0.addItem(self.ROIplot)
+        parent.p0.removeItem(parent.xp)
+        parent.p0.addItem(parent.xp)
+
+    def inROI(self, Y):
+        dists = np.zeros((Y.shape[0],))
+        for k,y in enumerate(Y):
+            dists[k] = (((self.positions - self.y)**2).sum(axis=1)**0.5).min()
+        inroi = dists < 0.5
+
+        return Y[inroi], dists[inroi]
+
+    def remove(self, parent):
+        '''remove ROI'''
+        parent.p0.removeItem(self.ROIplot)
+
 class gROI():
     '''
     draw a line segment which is the gradient over which to plot the points
@@ -21,7 +49,7 @@ def __init__(self, pos, prect, color, parent=None):
         self.d = ((prect[0][0,:] - prect[0][1,:])**2).sum()**0.5 / 2
         #self.slope = (pos[1,1] - pos[0,1]) / (pos[1,0] - pos[0,0])
         #self.yint  = pos[1,0] - self.slope * pos[0,0]
-        np.save('groi.npy', {'prect': self.prect, 'pos': self.pos})
+        #np.save('groi.npy', {'prect': self.prect, 'pos': self.pos})
         self.color = color
         self.pen = pg.mkPen(pg.mkColor(self.color),
                                 width=3,