adding 2D gaussian ROI fitting to settings windows

Author: SPENCE

choose_file_w_conda.bat docs/choose_file_w_conda.bat

@@ -45,7 +45,8 @@ class atom_window(QMainWindow):
     image_shape  -- shape of the images being taken, in pixels (x,y).
     name         -- an ID for this window, prepended to saved files.
     """
-    event_im = pyqtSignal(np.ndarray)
+    event_im = pyqtSignal(np.ndarray) # image taken by the camera as np array
+    roi_values = pyqtSignal(list) # list of ROIs (x, y, w, h, threshold)
 
     def __init__(self, last_im_path='.', rois=[(1,1,1,1)], num_plots=4, 
             image_shape=(512,512), name=''):
@@ -56,6 +57,7 @@ def __init__(self, last_im_path='.', rois=[(1,1,1,1)], num_plots=4,
         self.init_UI(num_plots) # adjust widgets from main_window
         self.event_im.connect(self.rh.process)
         self.event_im.connect(self.update_plots)
+        self.checking = False # whether the atom checker is active or not
 
     def init_UI(self, num_plots=4):
         """Create all the widgets and position them in the layout"""
@@ -123,14 +125,23 @@ def init_UI(self, num_plots=4):
             layout.addWidget(self.plots[-1], 1+(i//k)*3, 7+(i%k)*6, 2,6)  # allocate space in the grid
             try:
                 r = self.rh.ROIs[i]
-                remove_slot(r.threshedit.textEdited, self.update_plots, True)
                 self.plots[i].setTitle('ROI '+str(r.i))
                 # line edits with ROI x, y, w, h, threshold, auto update threshold
                 for j, label in enumerate(list(r.edits.values())+[r.threshedit, r.autothresh]): 
                     layout.addWidget(label, (i//k)*3, 7+(i%k)*6+j, 1,1)
             except IndexError as e: pass # logger.warning('Atom Checker has more plots than ROIs')
 
         self.display_rois() # put ROIs on the image
+
+        #### extra buttons ####
+        # send the ROIs used here to the image analysis settings window
+        self.roi_matching = QPushButton('Send ROIs to analysis', self)
+        self.roi_matching.clicked.connect(self.send_rois)
+        layout.addWidget(self.roi_matching, 2+num_plots//k*3,7, 1,1)
+        # the user can trigger the experiment early by pressing this button
+        self.trigger_button = QPushButton('Manual trigger experiment', self)
+        self.trigger_button.clicked.connect(self.send_trigger)
+        layout.addWidget(self.trigger_button, 2+num_plots//k*3,8, 1,1)
         #
         self.setWindowTitle(self.name+' - Atom Checker -')
         self.setWindowIcon(QIcon('docs/atomcheckicon.png'))
@@ -155,6 +166,14 @@ def user_roi(self, roi):
         for key, val in zip(r.edits.keys(), [xc, yc, w, h]):
             r.edits[key].setText(str(val))
 
+    def send_rois(self, toggle=0):
+        """Emit the signal with the list of ROIs"""
+        self.roi_values.emit([[r.x, r.y, r.w, r.h, r.t] for r in self.rh.ROIs])
+
+    def send_trigger(self, toggle=0):
+        """Emit the roi_handler's trigger signal to start the experiment"""
+        if self.checking: self.rh.trigger.emit(1)
+
     #### #### canvas functions #### ####
 
     def display_rois(self, n=''):
@@ -173,6 +192,7 @@ def display_rois(self, n=''):
         for i, r in enumerate(self.rh.ROIs):
             if r.roi not in viewbox.allChildren():
                 remove_slot(r.roi.sigRegionChangeFinished, self.user_roi, True) 
+                remove_slot(r.threshedit.textEdited, self.update_plots, True)
                 r.roi.setZValue(10)   # make sure the ROI is drawn above the image
                 viewbox.addItem(r.roi)
                 viewbox.addItem(r.label)

choose_file_w_enthought.bat docs/choose_file_w_enthought.bat

@@ -1,6 +1,6 @@
 pic_width=13
 pic_height=13
-ROIs=[[5, 7, 1, 1], [8, 7, 1, 1]]
+ROIs=[[3, 5, 1, 1, 30], [8, 7, 1, 1, 30]]
 bias=697
 image_path=.\\
 results_path=.\\

imageanalysis/atomChecker.py

@@ -21,6 +21,7 @@
 import logging
 logger = logging.getLogger(__name__)
 from maingui import int_validator, nat_validator
+from fitCurve import fit
 
 ####    ####    ####    ####
 
@@ -76,15 +77,42 @@ def create_rect_mask(self, image_shape=None):
         else: logger.warning('ROI tried to create invalid mask.\n' + 
             'shape %s, x %s, y %s, w %s, h %s'%(self.s, self.x, self.y, self.w, self.h))
 
-    def resize(self, xc, yc, width, height):
+    def create_gauss_mask(self, im=0):
+        """Fit a 2D Gaussian to the given image and use it to create a mask.
+        The Gaussian is fitted around the maximum intensity pixel."""
+        try:
+            if np.size(np.shape(im)) == 2:
+                self.s = np.shape(im)
+                self.mask = np.zeros(np.shape(im))
+                xc, yc = np.unravel_index(np.argmax(im), im.shape)
+                d = round(np.size(im[im > self.t])**0.5) # guess PSF size from pixels > threshold
+                im2 = im[xc-d:xc+d, yc-d:yc+d] # better for fitting to use zoom in
+                w = []
+                for i in range(2): # do Gaussian fit along each axis
+                    vals = np.sum(im2, axis=i)
+                    f = fit(np.arange(len(vals)), vals)
+                    f.estGaussParam()
+                    f.p0 = f.p0 + [np.min(vals)]
+                    f.getBestFit(f.offGauss) # only interested in the width
+                    w.append(round(f.ps[2]) if f.ps[2]>0 and np.isfinite(f.ps[2]) else 1) 
+                xy = np.meshgrid(list(reversed(range(-int(w[1]*2), int(w[1]*2)+1))), 
+                        range(-int(w[0]*2), int(w[0]*2)+1)) # make grid of (x,y) coordinates
+                # only include values of the Gaussian within 2 1/e^2 widths
+                self.mask[xc - int(w[0]*2) : xc + int(w[0]*2) + 1, 
+                    yc - int(w[1]*2) : yc + int(w[1]*2) + 1] = np.exp( # fill in 2D Gaussian
+                        -2*xy[0]**2 / w[0]**2 -2*xy[1]**2 / w[1]**2) /np.pi/w[0]/w[1]*2
+                self.resize(*map(int, [xc, yc, w[0], w[1]]), False) # update stored ROI values
+        except Exception as e: logger.error('ROI %s failed to set Gaussian mask\n'%self.i+str(e))
+    
+    def resize(self, xc, yc, width, height, create_sq_mask=True):
         """Reset the position and dimensions of the ROI"""
         self.x, self.y, self.w, self.h = xc, yc, width, height
         self.roi.setPos(xc - width//2, yc - height//2)
         self.roi.setSize((width, height))
         self.label.setPos(xc, yc)
         for key, val in zip(self.edits.keys(), [xc, yc, width, height]):
             self.edits[key].setText(str(val))
-        self.create_rect_mask()
+        if create_sq_mask: self.create_rect_mask()
 
     def atom(self):
         """A list of whether the counts are above threshold"""
@@ -131,11 +159,12 @@ class roi_handler(QWidget):
     im_shape -- dimensions of the image in pixels"""
     trigger = pyqtSignal(int)
 
-    def __init__(self, rois=[(1,1,1,1)], im_shape=(512,512)):
+    def __init__(self, rois=[(1,1,1,1,1)], im_shape=(512,512)):
         super().__init__()
         self.ROIs = [ROI(im_shape,*r, ID=i) for i, r in enumerate(rois)]
-        self.shape = im_shape
-        self.delim = ' '
+        self.shape = im_shape # image dimensions in pixels
+        self.bias  = 697      # bias offset to subtract from image counts
+        self.delim = ' '      # delimiter used to save/load files
 
     def create_rois(self, n):
         """Change the list of ROIs to have length n"""
@@ -146,7 +175,10 @@ def create_rois(self, n):
     def resize_rois(self, ROIlist):
         """Convenience function for setting multiple ROIs"""
         for i, roi in enumerate(ROIlist):
-            try: self.ROIs[i].resize(*roi)
+            try: 
+                self.ROIs[i].resize(*roi[:-1])
+                self.ROIs[i].t = roi[-1]
+                self.ROIs[i].threshedit.setText(str(roi[-1]))
             except (IndexError, ValueError) as e: logger.warning(
                 "Failed to resize ROI "+str(i)+": %s\n"%roi + str(e))
 
@@ -162,7 +194,7 @@ def process(self, im, include=True):
         success = 1
         for r in self.ROIs:
             try:
-                counts = np.sum(im * r.mask)
+                counts = np.sum(im * r.mask) - self.bias
                 success = 1 if abs(counts) // r.t and success else 0
                 r.c.append(counts) 
             except ValueError as e:
@@ -185,6 +217,10 @@ def set_pic_size(self, im_name):
         self.shape = np.genfromtxt(im_name, delimiter=self.delim).shape
         try: self.cam_pic_size_changed(self.shape[1]-1, self.shape[0])
         except IndexError: self.cam_pic_size_changed(self.shape[0]-1, 1)
+
+    def set_bias(self, bias):
+        """Update the bias offset subtracted from all image counts."""
+        self.bias = bias
 
     def cam_pic_size_changed(self, width, height):
         """Receive new image dimensions from Andor camera"""