improve perf of the viewver and correct bug in xls export

requirements.txt

 scikit-image
 h5py
 tifffile
-numpy
+numpy<1.20
 scipy
 pandas
+xlsxwriter
+ipywidgets
+ipympl

src/bactos_viewver.py

@@ -95,7 +95,7 @@ def compute_control_ratio(selected_file, ctrl_exp):
         The name of the control experiment (i.e. a hdf group name)
     """
 
-    positions = [p for p in range(load_image(selected_file, ctrl_exp).shape[1])]
+    positions = [p for p in range(get_stack_shape(selected_file, ctrl_exp)[1])]
     IF1c, IF2c = get_all_pos_fluo(selected_file, ctrl_exp, positions=positions)
         
     IF2c = np.hstack(IF2c)
@@ -447,6 +447,10 @@ class BactosViewver():
         self.update_intensity_tables()
         self.update_control_ratio_table()
         
+        # Need to init the first call of main figure to display it
+        with self.WplotAll:
+            plt.show(self.figure)
+            
     def build_explore_gui(self):
         """
         Build the main UI to explore the bacteria on images.
@@ -484,9 +488,9 @@ class BactosViewver():
         # Create a slider for experiment time
         self.t=widgets.IntSlider(min=0, max=max(self.times), step=1, description='time:')
         # Sliders for image intensity
-        self.F1minmax = widgets.IntRangeSlider(value=[0, 2**16], min=0, max=5000, 
+        self.F1minmax = widgets.IntRangeSlider(value=[0, 2000], min=0, max=2000, 
                                           description='F1:',orientation='horizontal')
-        self.F2minmax = widgets.IntRangeSlider(value=[0, 2**16], min=0, max=5000, 
+        self.F2minmax = widgets.IntRangeSlider(value=[0, 5000], min=0, max=5000, 
                                           description='F2:',orientation='horizontal')
         
         self.bactos_size_slider = widgets.FloatRangeSlider(value=[0.5, 15],
@@ -503,9 +507,9 @@ class BactosViewver():
         BTNfilters.on_click(self.on_filter_bactos)
         layoutfilters = widgets.VBox([self.bactos_size_slider, self.bactos_dist_slider, BTNfilters])
 
-        BTNexport = widgets.Button(description='Exporter vers Excel', button_style='success',
+        self.BTNexport = widgets.Button(description='Exporter vers Excel', button_style='success',
                                     layout=widgets.Layout(width='98%'))
-        BTNexport.on_click(self.on_export)
+        self.BTNexport.on_click(self.on_export)
         
         # Set Callback functions
         self.ListExp.observe(self.on_expe_changed, names='value')
@@ -544,7 +548,7 @@ class BactosViewver():
                                     #layout=widgets.Layout(width="20%")
                                     )
         else:
-            vcontrol = widgets.VBox([export_data_btn, self.ListExp, self.accordion, BTNexport],
+            vcontrol = widgets.VBox([export_data_btn, self.ListExp, self.accordion, self.BTNexport],
                                     #layout=widgets.Layout(width="20%")
                                     )
             
@@ -606,11 +610,11 @@ class BactosViewver():
         plt.close('bactostime')
         
         with self.WplotAll:
-            self.WplotAll.clear_output()
+            self.WplotAll.clear_output(wait=True)
             # Prevent autodisplay of mpl figures
             plt.ioff()
             self.figure = plt.figure('bactostime', figsize=(12,8))
-            display(self.figure.canvas)
+            #display(self.figure.canvas)
             plt.ion()
             # figure.canvas.layout.height = '800px' 
 
@@ -806,7 +810,7 @@ class BactosViewver():
 
         self.plimg1.set_data(self.selected_imgs[t, pos, z, :, :, self.drug_filter])
         self.plimg2.set_data(self.selected_imgs[t, pos, z, :, :, self.ctrl_filter])
-    
+        self.figure.canvas.draw_idle()
 
         if update_minmax:
             p0min, p0max = np.percentile(np.ma.masked_equal(self.selected_imgs[0, 0, 0, :, :, self.drug_filter], 0),
@@ -1001,7 +1005,10 @@ class BactosViewver():
 
         else:
             if self.ListExp.value != self.ListCtrl.value:
+                plt.ioff()
                 self.figure_all_pos = plt.figure('Plot all positions', figsize=(12,10))
+                plt.ion()
+                
                 G = plt.GridSpec(3,2, width_ratios=[1, 1/4])
                 ax1 = plt.subplot(G[0,1])
                 ax2 = plt.subplot(G[0,0])
@@ -1016,7 +1023,10 @@ class BactosViewver():
                 ax2.set_title('Fluo due à la drogue')
 
             else:
+                plt.ioff()
                 self.figure_all_pos = plt.figure('Plot all positions', figsize=(12,7))
+                plt.ion()
+                
                 G = plt.GridSpec(2,1)
                 ax3 = plt.subplot(G[0,0])
                 ax4 = plt.subplot(G[1,0], sharex=ax3)
@@ -1111,7 +1121,7 @@ class BactosViewver():
         
             if ctrl_exp is not None and ctrl_exp != exp:
                 exp_all_drug = []
-                positions = [p for p in range(load_image(self.selected_file, exp).shape[1])]
+                positions = [p for p in range(get_stack_shape(self.selected_file, exp)[1])]
                 for pos in positions:
                     drug = load_drug_signal(self.selected_file, exp, pos)
                     SelectB = load_selected_bactos(self.selected_file, exp, pos)
@@ -1658,6 +1668,7 @@ class BactosViewver():
         Export the h5file data to excel.
         """
 
+        self.BTNexport.disabled = True
         # Output file name (should be the same as the imput source)
         fout = os.path.abspath(self.source_file)
         fout = os.path.splitext(fout)[0] + '.xlsx'
@@ -1667,7 +1678,7 @@ class BactosViewver():
                 ctrl_exp = load_control_exp(self.selected_file, expe)
                 row = -1 # init raw at -1 (if no bacteria on position 1 set the
                          # position 2 on top of Excel sheet)
-                positions = [p for p in range(load_image(self.selected_file, expe).shape[1])]
+                positions = [p for p in range(get_stack_shape(self.selected_file, expe)[1])]
                 srow = 0
 
                 # Test if it's a time or static
@@ -1676,6 +1687,25 @@ class BactosViewver():
                 else:
                     istime = False
                    
+                #Crop name if too long >31
+                if len(expe)>31:
+                    sname = expe[:31]
+                else:
+                    sname = expe
+
+                # Excel sheet need to have unik lower case name
+                if sname.lower() in prevsname:
+                    try:
+                        tmpind = int(sname[0])
+                    except:
+                        tmpind = 1
+                                
+                    sname = str(tmpind+1) + '_' + sname
+                    sname = sname[:31]            
+                    
+                prevsname += [sname.lower()]
+                # print(prevsname)
+                
                 for pos in positions:
                     selectedB = load_selected_bactos(self.selected_file,
                                                      expe, pos)
@@ -1697,12 +1727,6 @@ class BactosViewver():
 
                         row, col = Area.shape
                         
-                        #Crop name if too long >31
-                        if len(expe)>31:
-                            sname = expe[:31]
-                        else:
-                            sname = expe
-
                         Area.to_excel(writer, sheet_name=sname,
                                       header=head, startrow=srow)
 
@@ -1715,6 +1739,7 @@ class BactosViewver():
                         if ctrl_exp != expe:
                             Idrug = create_idrug_pandas(self.selected_file,
                                                         expe, pos, selectedB)
+                            if Idrug is not None:
                                 Idrug.to_excel(writer, sheet_name=sname,
                                                index=False, header=head,
                                                startcol=col+2+(col2+1)*2,
@@ -1735,6 +1760,7 @@ class BactosViewver():
                 if selectedB is not None and expe == ctrl_exp:
                     F2F1 = create_control_ratio_pandas(self.selected_file,
                                                        expe, positions)
+                    if F2F1 is not None:
                         F2F1.to_excel(writer, sheet_name=sname,
                                       index=True, startcol=col+2+(col2+1)*2)
                    
@@ -1763,9 +1789,6 @@ class BactosViewver():
                         worksheet.insert_chart(line+5, col+2+(col2+1)*2, chart3)
                 else:
                     # If no data for this experiment create an empty sheet
-                    if len(expe) > 31:
-                        sname = expe[:31]
-                    else:
-                        sname = expe
-
                     writer.book.add_worksheet(sname)
+                    
+        self.BTNexport.disabled = False

src/lib_bactos_hdf.py

@@ -77,6 +77,25 @@ def load_mask(data_in, expe_name, pos):
         
     return output
 
+def get_stack_shape(data_in, expe_name):
+    """
+    Get the dimensions of the image stack for this "expe_name" in the data_in HDF file.
+
+    Parameters:
+    -----------
+
+    - data_in, str:
+        the path to the h5file.
+
+    - expe_name, str:
+        the name of the experiment.
+
+    Return the shape of the image stack
+    """
+    with h5py.File(data_in, 'r') as f:
+        output = f[expe_name]['images'].shape
+        
+    return output
 
 def load_intensity_profile(data_in, expe_name, channel, pos):
     """