This brings in the channel swapping function

mac/pyrgb/display/rgbdisplay.py

@@ -109,15 +109,18 @@ def __init__(self, argv):
         self.lay_inputs.addWidget(self.p0label, 0, 4)
         self.p0 = QtGui.QComboBox()
         self.lay_inputs.addWidget(self.p0, 0, 5)
+        self.p0.activated.connect( self.changeChannelViewed )
 
         self.p1label = QtGui.QLabel("G:")
         self.lay_inputs.addWidget(self.p1label, 1, 4)
         self.p1 = QtGui.QComboBox()
+        self.p1.activated.connect( self.changeChannelViewed )
         self.lay_inputs.addWidget(self.p1, 1, 5)
 
         self.p2label = QtGui.QLabel("B:")
         self.lay_inputs.addWidget(self.p2label, 2, 4)
         self.p2 = QtGui.QComboBox()
+        self.p2.activated.connect( self.changeChannelViewed )
         self.lay_inputs.addWidget(self.p2, 2, 5)
 
         self.planes = [self.p0, self.p1, self.p2]
@@ -385,7 +388,6 @@ def plotData(self):
 
         # update channel combo boxes
         nchs = self.dm.get_nchannels(event, self.image_producer)
-        print "Set the RGB drop boxes: ", nchs, " current count=", self.p0.count()
         if self.p0.count() != (nchs + 1):
             self.p0.clear()
             self.p1.clear()
@@ -472,15 +474,15 @@ def regionChanged(self):
 
         # use mask to updated only pixels not already updated
         if self.cv2_layout.overwrite == False:
-            self.image.orig_mat[idx] = pcopy[idx]
+            self.image.orig_mat[idx] = pcopy[idx] # reverts prev. modified pixels, preventing double change
             self.modimage[sl] = 1
 
         if self.cv2_layout.transform == False:
             return
 
         self.pimg = self.image.set_plot_mat(self.iimin,self.iimax)  
 
-        self.imi.setImage(self.pimg)
+        self.imi.setImage(self.pimg) # send it back to the viewer
 
         # For now this is fine....
 
@@ -552,6 +554,11 @@ def drawBBOX(self, kType):
                 self.plt.addItem(r1)
                 self.boxes.append(r1)
 
+    def changeChannelViewed(self):
+        self.setViewPlanes()
+        self.pimg = self.image.swap_plot_mat( self.iimin, self.iimax, self.views )
+        self.imi.setImage(self.pimg)
+
     def load_current_image(self):
         print "Loading current image!"
         # revert the image back to Image2D.nd_array style (possibly

mac/pyrgb/lib/datamanager.py

@@ -40,18 +40,19 @@ def get_nchannels(self,ii,imgprod) :
         imdata  = self.iom.get_data(larcv.kProductImage2D,imgprod)
         return imdata.Image2DArray().size()
 
-    def get_event_image(self,ii,imgprod,roiprod,planes) :
+    def get_event_image(self,ii,imgprod,roiprod,planes, refresh=True) :
 
         #Load data in TChain
         self.iom.read_entry(ii)
-
+        
         hasroi = False
         if roiprod is not None:
             roidata = self.iom.iom.get_data(larcv.kProductROI,roiprod)
             roidata = roidata.ROIArray()
             hasroi = True
 
-        imdata  = self.iom.get_data(larcv.kProductImage2D,imgprod)
+
+        imdata  = self.iom.get_data(larcv.kProductImage2D,imgprod) # goes to disk
 
         self.run    = imdata.run()
         self.subrun = imdata.subrun()

mac/pyrgb/lib/image_types/ch12image.py

@@ -3,28 +3,64 @@
 
 
 class Ch12Image(PlotImage):
+    # notes
+    # orig_mat is the ndarray representation of image2d data
+    # plot_mat is modified to have overlays
+    # when loading, we manip orig_mat to have the orientation we want
+    # before going to caffe, __revert_image__ is called to rearrange the image
 
     def __init__(self, img_v, roi_v, planes):
         super(Ch12Image, self).__init__(img_v, roi_v, planes)
         self.name = "Ch12Image"
 
     def __create_mat__(self):
 
-        # compressed images all have the same shape
+        # this 12 ch data (from the lmdb) was made before the current convention
+        # thus it stores its data in time order (rather than reverse time order)
+        # it also has transposed the matrix
+        # to make sure the final orientation that is sent to caffe 
+        # is correct while also keeping to this display's conventions
+        #  we 1) do not time reverse it, 2) then transpose
+        # tmw has checked that this is correct
+
+        # working copy
+        if not hasattr(self,'work_mat'):
+            self.work_mat = np.zeros(list(self.img_v[0].shape)+[len(self.img_v)])
+
+        #compressed images all have the same shape
         self.orig_mat = np.zeros(list(self.img_v[0].shape) + [3])
 
         for p, fill_ch in enumerate(self.planes):
-
+            self.work_mat[:,:,p] = self.img_v[fill_ch]
             if fill_ch == -1: continue
-
             self.orig_mat[:, :, p] = self.img_v[fill_ch]
-
             self.idx[fill_ch] = p
 
-        self.orig_mat = self.orig_mat[:, ::-1, :]
+        #self.orig_mat = self.orig_mat[:, ::-1, :]
+        self.work_mat = np.transpose( self.work_mat, (1,0,2) )
+        self.orig_mat = np.transpose( self.orig_mat, (1,0,2) )
+
+
+    def __swap_mat_channels__(self,imin,imax,newchs):
+        print "swap channels to: ",newchs
+        # store the current state of the orig_mat into the working matrix
+        for p,ch in enumerate(self.planes):
+            if ch!=-1:
+                self.work_mat[:,:,ch] = self.orig_mat[:,:,p] # don't put a blank in there
+        # swap the planes
+        self.planes = newchs
+        # put work mat values into orig_mat
+        for p,ch in enumerate(self.planes):
+            if ch!=-1:
+                self.orig_mat[:,:,p] = self.work_mat[:,:,ch]
+            else:
+                self.orig_mat[:,:,p] = np.zeros( (self.orig_mat.shape[0],self.orig_mat.shape[1] ) )
+        # make the viewing plot_mat and return
+        return self.__set_plot_mat__(imin,imax)
 
     def __set_plot_mat__(self, imin, imax):
 
+
         self.plot_mat = self.orig_mat.copy()
 
         # do contrast thresholding
@@ -40,7 +76,7 @@ def __set_plot_mat__(self, imin, imax):
 
     # revert back to how image was in ROOTFILE for caffe...
     def __revert_image__(self): 
-        self.orig_mat = self.orig_mat[:,::-1,:]    
+        self.orig_mat = np.transpose( self.orig_mat, (1,0,2) )
 
     def __create_rois__(self):
 

mac/pyrgb/lib/image_types/plotimage.py

@@ -74,6 +74,10 @@ def __revert_image__(self):
     def set_plot_mat(self,imin,imax):
         return self.__set_plot_mat__(imin,imax)
 
+    # rswap channels that are shown
+    def swap_plot_mat(self,imin,imax,planes):
+        return self.__swap_mat_channels__(imin,imax,planes)
+
     # create the ROIs if they exists and return them
     def parse_rois(self):
         self.__create_rois__()

mac/pyrgb/rgb_caffe/testwrapper.py

@@ -112,8 +112,8 @@ def prep_image(self):
             im[:,:,ix] -= mean
 
         #image is already thresholded according to the user
-        im[ im < self.config['imin'] ] = self.config['imin']
-        im[ im > self.config['imax'] ] = self.config['imax']
+        #im[ im < self.config['imin'] ] = self.config['imin']
+        #im[ im > self.config['imax'] ] = self.config['imax']
 
         return im
 
@@ -152,6 +152,16 @@ def forward_result(self):
 
         self.scores = scores
         print "Scores:  {}".format(scores)
+
+        if "save_datablob" in self.config and self.config["save_datablob"]==True:
+            print "SAVING DATA BLOB TO FILE"
+            # we dump the data array the network has in it's blob to a numpy binary file
+            # this is useful for sanity-checks
+            if not hasattr(self,'data_numpy_outfile'):
+                self.data_numpy_outfile = file('saved_data_blobs.npz','w')
+            data_blob = self.net.blobs["data"].data
+            np.savez( self.data_numpy_outfile, data_blob )
+
 
 
     def __generate_model__(self):

mac/ubresnet_12ch_768.yml

@@ -46,3 +46,6 @@ lastfc: probt
 
 # This layer doesn't have to be here but that's OK, what is the name of the loss layer
 loss: loss
+
+# For Debug: save the data given to the network in a numpy binary file
+save_datablob: True