Spectrometer pr v1

config/example/default.cfg

@@ -93,10 +93,11 @@ hardware:
                 - 'Very long name of a random state'
                 - 'Another very long name of a random state'
 
-    myspectrometer:
-        module.Class: 'spectrometer.spectrometer_dummy.SpectrometerInterfaceDummy'
-        connect:
-            fitlogic: 'fitlogic'
+    science_camera_dummy:
+        module.Class: 'dummies.science_camera_dummy.Main'
+
+    grating_spectrometer_dummy:
+        module.Class: 'dummies.grating_spectrometer_dummy.Main'
 
     motordummy:
         module.Class: 'motor.motor_dummy.MotorDummy'
@@ -310,14 +311,6 @@ logic:
         save_pdf: True
         save_png: True
 
-    spectrumlogic:
-        module.Class: 'spectrum.SpectrumLogic'
-        connect:
-            spectrometer: 'myspectrometer'
-            savelogic: 'savelogic'
-            odmrlogic: 'odmrlogic' # optional
-            fitlogic: 'fitlogic'
-
     magnet_logic:
         module.Class: 'magnet_logic.MagnetLogic'
         connect:
@@ -372,6 +365,13 @@ logic:
             hardware: 'cameradummy'
             savelogic: 'savelogic'
 
+    spectrumlogic:
+        module.Class: 'spectrum_logic.SpectrumLogic'
+        connect:
+            spectrometer: 'grating_spectrometer_dummy'
+            camera: 'science_camera_dummy'
+            savelogic: 'savelogic'
+
 gui:
     tray:
         module.Class: 'trayicon.TrayIcon'
@@ -431,11 +431,6 @@ gui:
         connect:
             automationlogic: 'automationlogic'
 
-    spectrometer:
-        module.Class: 'spectrometer.spectrometergui.SpectrometerGui'
-        connect:
-            spectrumlogic: 'spectrumlogic'
-
     pulsedmeasurement:
         module.Class: 'pulsed.pulsed_maingui.PulsedMeasurementGui'
         connect:
@@ -509,3 +504,9 @@ gui:
         module.Class: 'counter.countergui.CounterGui'
         connect:
             counterlogic1: 'counterlogic'
+
+    spectrometer:
+        module.Class: 'spectrometer.spectrometer.Main'
+        connect:
+            spectrumlogic: 'spectrumlogic'
+            savelogic: 'savelogic'

documentation/changelog.md

@@ -93,6 +93,8 @@ please use _ni_x_series_in_streamer.py_ as hardware module.
 * Added custom circular loading indicator widget `qtwidgets.loading_indicator.CircleLoadingIndicator`
 * added property disable_wheel to custom ScienSponBox and ScienDSpinBox to deactivate wheel scrolling if required
 * Added possibility to fit data of all ranges in ODMR module when Fit range is -1
+* Added new dummy/interface/logic/gui chain for scientific spectrometer
+* Added new spectrometer and camera hardware modules for andor devices
 
 
 Config changes:

gui/gui_components/colorbar/colorbar.py

@@ -0,0 +1,166 @@
+# -*- coding: utf-8 -*-
+"""
+This module contains a GUI component to crate easily a colorbar in any GUI module
+
+Qudi is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+Qudi is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with Qudi. If not, see <http://www.gnu.org/licenses/>.
+
+Copyright (c) the Qudi Developers. See the COPYRIGHT.txt file at the
+top-level directory of this distribution and at <https://github.com/Ulm-IQO/qudi/>
+"""
+
+import os
+import pyqtgraph as pg
+from functools import partial
+
+from gui.colordefs import QudiPalettePale as Palette
+from gui.guibase import GUIBase
+from gui.colordefs import ColorScaleInferno
+from qtwidgets.scientific_spinbox import ScienDSpinBox, ScienSpinBox
+
+from qtpy import QtWidgets
+from qtpy import uic
+from gui.guiutils import ColorBar
+from gui.colordefs import ColorScaleMagma
+
+import numpy as np
+
+import time
+
+class ColorbarWidget(QtWidgets.QWidget):
+    """ Create the widget, based on the corresponding *.ui file."""
+
+    def __init__(self, image_widget, unit='c/s'):
+        # Get the path to the *.ui file
+        this_dir = os.path.dirname(__file__)
+        ui_file = os.path.join(this_dir, 'ui_colorbar.ui')
+
+        # Load it
+        super(ColorbarWidget, self).__init__()
+        uic.loadUi(ui_file, self)
+
+        self._cb_min = 0
+        self._cb_max = 100
+        self.unit = unit
+
+        self.init_spin_box()
+        self.init_colorbar()
+
+        self.set_image(image_widget)
+
+        self.percentile.clicked.emit()
+        self.percentile.setChecked(True)
+
+    def init_spin_box(self):
+        """ Initialize all the spinboxes """
+        self._min_percentile = ScienDSpinBox()
+        self._min_manual = ScienDSpinBox()
+        self._max_percentile = ScienDSpinBox()
+        self._max_manual = ScienDSpinBox()
+
+        self._min_percentile.setSuffix('%')
+        self._min_percentile.setMinimum(0)
+        self._min_percentile.setMaximum(100)
+        self._min_percentile.setValue(0)
+
+        self._min_manual.setSuffix(self.unit)
+
+        self._max_percentile.setSuffix('%')
+        self._max_percentile.setMinimum(0)
+        self._max_percentile.setMaximum(100)
+        self._max_percentile.setValue(100)
+
+        self._max_manual.setSuffix(self.unit)
+
+        self.min.addWidget(self._min_manual)
+        self.min.addWidget(self._min_percentile)
+        self.max.addWidget(self._max_percentile)
+        self.max.addWidget(self._max_manual)
+
+        self._min_percentile.valueChanged.connect(self.shortcut_to_cb_centiles)
+        self._min_manual.valueChanged.connect(self.shortcut_to_cb_manual)
+        self._max_percentile.valueChanged.connect(self.shortcut_to_cb_centiles)
+        self._max_manual.valueChanged.connect(self.shortcut_to_cb_manual)
+
+        self.manual.clicked.connect(self.update_cb_range)
+        self.percentile.clicked.connect(self.update_cb_range)
+
+    def init_colorbar(self):
+        """ Create the colorbar """
+        self.my_colors = ColorScaleInferno()
+        self._color_map = ColorScaleMagma()
+        self._cb = ColorBar(self.my_colors.cmap_normed, width=100, cb_min=self._cb_min, cb_max=self._cb_max)
+        self.colorbar.addItem(self._cb)
+        self.colorbar.hideAxis('bottom')
+        self.colorbar.setLabel('left', 'Intensity', units=self.unit)
+        self.colorbar.setMouseEnabled(x=False, y=False)
+
+    def set_image(self, image_widget):
+        """ Set the image widget associated to the colorbar """
+        self._image = image_widget
+        self._min_manual.setValue(np.min(self._image.image))
+        self._min_percentile.setValue(0)
+        self._max_manual.setValue(np.max(self._image.image))
+        self._max_percentile.setValue(100)
+        self.refresh_colorbar()
+
+    def get_cb_range(self):
+        """ Determines the cb_min and cb_max values for the image """
+        # If "Manual" is checked, or the image data is empty (all zeros), then take manual cb range.
+        if self.manual.isChecked() or np.count_nonzero(self._image.image) < 1:
+            cb_min = self._min_manual.value()
+            cb_max = self._max_manual.value()
+
+        # Otherwise, calculate cb range from percentiles.
+        else:
+            # Exclude any zeros (which are typically due to unfinished scan)
+            image_nonzero = self._image.image[np.nonzero(self._image.image)]
+
+            # Read centile range
+            low_centile = self._min_percentile.value()
+            high_centile = self._max_percentile.value()
+
+            cb_min = np.percentile(image_nonzero, low_centile)
+            cb_max = np.percentile(image_nonzero, high_centile)
+
+        cb_range = [cb_min, cb_max]
+
+        return cb_range
+
+    def refresh_colorbar(self):
+        """ Adjust the colorbar. """
+        cb_range = self.get_cb_range()
+        self._cb.refresh_colorbar(cb_range[0], cb_range[1])
+
+    def refresh_image(self):
+        """ Update the image colors range."""
+
+        image_data = self._image.image
+        cb_range = self.get_cb_range()
+        self._image.setImage(image=image_data, levels=(cb_range[0], cb_range[1]))
+        self.refresh_colorbar()
+
+    def update_cb_range(self):
+        """ Redraw colour bar and image."""
+        self.refresh_colorbar()
+        self.refresh_image()
+
+    def shortcut_to_cb_manual(self):
+        """ Someone edited the absolute counts range for the colour bar, better update."""
+        self.manual.setChecked(True)
+        self.update_cb_range()
+
+    def shortcut_to_cb_centiles(self):
+        """Someone edited the centiles range for the colour bar, better update."""
+        self.percentile.setChecked(True)
+        self.update_cb_range()

gui/gui_components/colorbar/ui_colorbar.ui

@@ -0,0 +1,98 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>colorbarWidget</class>
+ <widget class="QWidget" name="colorbarWidget">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>93</width>
+    <height>584</height>
+   </rect>
+  </property>
+  <property name="sizePolicy">
+   <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
+    <horstretch>0</horstretch>
+    <verstretch>0</verstretch>
+   </sizepolicy>
+  </property>
+  <property name="maximumSize">
+   <size>
+    <width>93</width>
+    <height>16777215</height>
+   </size>
+  </property>
+  <property name="font">
+   <font>
+    <pointsize>8</pointsize>
+   </font>
+  </property>
+  <property name="windowTitle">
+   <string>Form</string>
+  </property>
+  <layout class="QVBoxLayout" name="verticalLayout">
+   <item>
+    <layout class="QVBoxLayout" name="max"/>
+   </item>
+   <item>
+    <layout class="QVBoxLayout" name="min">
+     <item>
+      <widget class="PlotWidget" name="colorbar">
+       <property name="maximumSize">
+        <size>
+         <width>100</width>
+         <height>16777215</height>
+        </size>
+       </property>
+      </widget>
+     </item>
+    </layout>
+   </item>
+   <item>
+    <widget class="QRadioButton" name="percentile">
+     <property name="sizePolicy">
+      <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+       <horstretch>0</horstretch>
+       <verstretch>0</verstretch>
+      </sizepolicy>
+     </property>
+     <property name="font">
+      <font>
+       <pointsize>8</pointsize>
+      </font>
+     </property>
+     <property name="text">
+      <string>Percentiles</string>
+     </property>
+    </widget>
+   </item>
+   <item>
+    <widget class="QRadioButton" name="manual">
+     <property name="sizePolicy">
+      <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+       <horstretch>0</horstretch>
+       <verstretch>0</verstretch>
+      </sizepolicy>
+     </property>
+     <property name="font">
+      <font>
+       <pointsize>8</pointsize>
+      </font>
+     </property>
+     <property name="text">
+      <string>Manual</string>
+     </property>
+    </widget>
+   </item>
+  </layout>
+ </widget>
+ <customwidgets>
+  <customwidget>
+   <class>PlotWidget</class>
+   <extends>QGraphicsView</extends>
+   <header location="global">pyqtgraph</header>
+  </customwidget>
+ </customwidgets>
+ <resources/>
+ <connections/>
+</ui>