Bugfix/dark pixels

README.rst

@@ -20,6 +20,7 @@ Authors
 
 * Sebastien J. Weber
 * Nicolas Tappy
+* Arnaud Meyer
 
 Instruments
 ===========

src/pymodaq_plugins_oceaninsight/daq_viewer_plugins/plugins_1D/daq_1Dviewer_Seabreeze.py

@@ -12,14 +12,15 @@
 
 
 class DAQ_1DViewer_Seabreeze(DAQ_Viewer_base):
-    """
-    """
+    """PyMoDAQ 1DViewer class for devices supported by the Seabreeze library."""
+
     # Upon initialisation
     devices = list_devices()
 
-    #Supports pseudo hardware-averaging
+    # Supports pseudo hardware-averaging
     hardware_averaging = True
 
+    # Adjustable parameters
     params = comon_parameters + [
         {'title': 'Device:', 'name': 'device', 'type': 'list', 'limits': devices},
         {'title': 'Integration (ms):', 'name': 'integration', 'type': 'float', 'value': 1.0},
@@ -28,7 +29,7 @@ class DAQ_1DViewer_Seabreeze(DAQ_Viewer_base):
             {'title': 'Non Linearity correction:', 'name': 'correct_non_linearity', 'type': 'bool', 'value': False},
             {'title': 'Max Intensity', 'name': 'max_intensity', 'type': "float", 'value': 65535, 'readonly': True},
             {'title': 'Pixels:', 'name': 'pixels', 'type': 'int', 'value': 2048, 'readonly': True},
-            {'title': 'Dark Channels:', 'name': 'dark_channels', 'type': 'int', 'value': 10, 'readonly': True},
+            {'title': 'Dark Channels:', 'name': 'dark_channels', 'type': 'str', 'value': '', 'readonly': True},
             {'title': 'Readout Time (ms)', 'name': 'readout_time', 'type': 'float', 'value': 666, 'readonly': True},
         ]}
     ]
@@ -59,23 +60,27 @@ def ini_detector(self, controller=None):
             * controller (object) initialized controller
             *initialized: (bool): False if initialization failed otherwise True
         """
-        self.ini_detector_init(controller, None)
-
         if self.is_master:
             # From what I understand this will just get the spectro currently selected in the list
             dvc = self.settings['device']
             self.controller = Spectrometer(dvc)
-            self.controller.open()
-            #####################################
+            #self.controller.open()
+
+        else:
+            self.controller = controller
 
         # Oceanoptics spectrometers (at least the ones i Know) have fixed axis
-        # get inactive pixels
-        c0 = self.controller.f.spectrometer.get_electric_dark_pixel_indices()[-1]
-        self.settings.child('advanced').child('dark_channels').setValue(c0)
+        # get index of inactive pixels
+        dark_indices = self.controller.f.spectrometer.get_electric_dark_pixel_indices()
+        self.settings.child('advanced').child('dark_channels').setValue(", ".join([str(x) for x in dark_indices]))
         # get the x_axis
         data_x_axis = self.controller.wavelengths()  # Way to get the x axis
-        data_x_axis = data_x_axis[c0:] * 1e9  # Get rid of the dark pixels
-        self.x_axis = Axis(data=data_x_axis, label='wavelength', units='m', index=0)
+        # keep range without dark pixels
+        x_indices = np.arange(data_x_axis.shape[0])
+        self.valid_range = np.setdiff1d(x_indices, dark_indices)
+        data_x_axis = data_x_axis[self.valid_range]
+        # generate PyMoDAQ axis
+        self.x_axis = Axis(data=data_x_axis * 1e-9, label='wavelength', units='m', index=0)
 
         # Get the name
         specname = f"Ocean Insight {self.controller.model}"
@@ -134,16 +139,18 @@ def grab_data(self, Naverage = 1, **kwargs):
         kwargs: (dict) of others optionals arguments
         """
         nlc = self.settings.child('advanced').child('correct_non_linearity').value()
-        c0 = self.settings.child('advanced').child('dark_channels').value()
+        #c0 = self.settings.child('advanced').child('dark_channels').value()
+
         # synchrone version (blocking function)
         # Pseudo-hardware-averaging
         if Naverage > 1:
-            data = [self.controller.intensities(correct_nonlinearity=nlc)[c0:] for i in range(Naverage)]
+            data = [self.controller.intensities(correct_nonlinearity=nlc)[self.valid_range]
+                    for i in range(Naverage)]
             data = np.array(data)
             data = data.mean(0)
         # Otherwise normal single-acquisition
         else:
-            data = self.controller.intensities(correct_nonlinearity=nlc)[c0:]
+            data = self.controller.intensities(correct_nonlinearity=nlc)[self.valid_range]
 
         self.dte_signal.emit(DataToExport('Spectro', data=[
             DataFromPlugins(name='oceanseabreeze', data=[data], dim='Data1D',