diff --git a/.idea/workspace.xml b/.idea/workspace.xml
index 16d701d..1005ace 100644
--- a/.idea/workspace.xml
+++ b/.idea/workspace.xml
@@ -1,36 +1,18 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <project version="4">
   <component name="ChangeListManager">
-    <list default="true" id="68ddce6f-baaa-4bac-af24-443b9be545bf" name="Changes" comment="Debug for calculating atom number.&#10;&#10;Add background subtraction function.&#10;&#10;Correct the pixel size of the camera">
-      <change afterPath="$PROJECT_DIR$/HelperClasses/Plotting/DataExtractorLyse.py" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/HelperClasses/Plotting/MainPlotPanel.py" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/HelperClasses/Plotting/PlottingData.py" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/HelperClasses/Plotting/PlottingPanel.py" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/HelperClasses/Plotting/Quick1DPlot.py" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/HelperClasses/Plotting/Unknown.py" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/HelperClasses/Plotting/WidgetDataSelector.py" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/HelperClasses/Plotting/WidgetFakeColorPlot.py" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/HelperClasses/Plotting/WidgetPlot.py" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/HelperClasses/Plotting/WidgetQuick2DPlot.py" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/HelperClasses/Plotting/WidgetQuickPlotGenerator.py" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/HelperClasses/Plotting/WidgetQuickWaterFlowPlot.py" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/HelperClasses/Plotting/__init__.py" afterDir="false" />
-      <change afterPath="$PROJECT_DIR$/test_living_plot.py" afterDir="false" />
+    <list default="true" id="68ddce6f-baaa-4bac-af24-443b9be545bf" name="Changes" comment="Update for plotting function.">
+      <change afterPath="$PROJECT_DIR$/HelperClasses/Plotting/WidgetAnalysePanel.py" afterDir="false" />
       <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/__init__.py" beforeDir="false" afterPath="$PROJECT_DIR$/__init__.py" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/build/lib/dylab/AbsorptionImaging.py" beforeDir="false" afterPath="$PROJECT_DIR$/build/lib/dylab/AbsorptionImaging.py" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/build/lib/dylab/DyTransition.py" beforeDir="false" afterPath="$PROJECT_DIR$/build/lib/dylab/DyTransition.py" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/build/lib/dylab/Fitting.py" beforeDir="false" afterPath="$PROJECT_DIR$/build/lib/dylab/Fitting.py" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/dylab/AbsorptionImaging.py" beforeDir="false" afterPath="$PROJECT_DIR$/HelperClasses/AbsorptionImaging.py" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/dylab/Camera.py" beforeDir="false" afterPath="$PROJECT_DIR$/HelperClasses/Camera.py" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/dylab/DyTransition.py" beforeDir="false" afterPath="$PROJECT_DIR$/HelperClasses/DyTransition.py" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/dylab/Fitting.py" beforeDir="false" afterPath="$PROJECT_DIR$/HelperClasses/Fitting.py" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/dylab/FittingFunction.py" beforeDir="false" afterPath="$PROJECT_DIR$/HelperClasses/FittingFunction.py" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/dylab/TransitionClass.py" beforeDir="false" afterPath="$PROJECT_DIR$/HelperClasses/TransitionClass.py" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/dylab/__init__.py" beforeDir="false" afterPath="$PROJECT_DIR$/HelperClasses/__init__.py" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/setup.py" beforeDir="false" afterPath="$PROJECT_DIR$/setup.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/HelperClasses/AbsorptionImaging.py" beforeDir="false" afterPath="$PROJECT_DIR$/HelperClasses/AbsorptionImaging.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/HelperClasses/Plotting/DataExtractorLyse.py" beforeDir="false" afterPath="$PROJECT_DIR$/HelperClasses/Plotting/DataExtractorLyse.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/HelperClasses/Plotting/MainPlotPanel.py" beforeDir="false" afterPath="$PROJECT_DIR$/HelperClasses/Plotting/MainPlotPanel.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/HelperClasses/Plotting/WidgetDataSelector.py" beforeDir="false" afterPath="$PROJECT_DIR$/HelperClasses/Plotting/WidgetDataSelector.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/HelperClasses/Plotting/WidgetFakeColorPlot.py" beforeDir="false" afterPath="$PROJECT_DIR$/HelperClasses/Plotting/WidgetFakeColorPlot.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/HelperClasses/Plotting/WidgetPlot.py" beforeDir="false" afterPath="$PROJECT_DIR$/HelperClasses/Plotting/WidgetPlot.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/test.py" beforeDir="false" afterPath="$PROJECT_DIR$/test.py" afterDir="false" />
       <change beforePath="$PROJECT_DIR$/test_absorption_imaging.py" beforeDir="false" afterPath="$PROJECT_DIR$/test_absorption_imaging.py" afterDir="false" />
-      <change beforePath="$PROJECT_DIR$/test_fitting.py" beforeDir="false" afterPath="$PROJECT_DIR$/test_fitting.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/test_living_plot.py" beforeDir="false" afterPath="$PROJECT_DIR$/test_living_plot.py" afterDir="false" />
     </list>
     <option name="SHOW_DIALOG" value="false" />
     <option name="HIGHLIGHT_CONFLICTS" value="true" />
@@ -47,6 +29,14 @@
   <component name="Git.Settings">
     <option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$" />
   </component>
+  <component name="GitSEFilterConfiguration">
+    <file-type-list>
+      <filtered-out-file-type name="LOCAL_BRANCH" />
+      <filtered-out-file-type name="REMOTE_BRANCH" />
+      <filtered-out-file-type name="TAG" />
+      <filtered-out-file-type name="COMMIT_BY_MESSAGE" />
+    </file-type-list>
+  </component>
   <component name="ProjectId" id="2CCrwoItH5rBCZFtzaw6hxgrIjy" />
   <component name="ProjectViewState">
     <option name="hideEmptyMiddlePackages" value="true" />
@@ -64,8 +54,8 @@
       <recent name="D:\Jianshun Gao\Simulations\DyLab\publishedPackage\dylab\HelperClasses\Plotting" />
     </key>
   </component>
-  <component name="RunManager" selected="Python.test_living_plot">
-    <configuration name="Plotting" type="PythonConfigurationType" factoryName="Python" temporary="true" nameIsGenerated="true">
+  <component name="RunManager" selected="Python.test (1)">
+    <configuration name="Plotting1" type="PythonConfigurationType" factoryName="Python" temporary="true" nameIsGenerated="true">
       <module name="dylab" />
       <option name="INTERPRETER_OPTIONS" value="" />
       <option name="PARENT_ENVS" value="true" />
@@ -78,7 +68,29 @@
       <option name="ADD_CONTENT_ROOTS" value="true" />
       <option name="ADD_SOURCE_ROOTS" value="true" />
       <EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" />
-      <option name="SCRIPT_NAME" value="$PROJECT_DIR$/HelperClasses/Plotting.py" />
+      <option name="SCRIPT_NAME" value="D:\Jianshun Gao\Simulations\DyLab\publishedPackage\dylab\HelperClasses\Plotting1.py" />
+      <option name="PARAMETERS" value="" />
+      <option name="SHOW_COMMAND_LINE" value="false" />
+      <option name="EMULATE_TERMINAL" value="false" />
+      <option name="MODULE_MODE" value="false" />
+      <option name="REDIRECT_INPUT" value="false" />
+      <option name="INPUT_FILE" value="" />
+      <method v="2" />
+    </configuration>
+    <configuration name="test (1)" type="PythonConfigurationType" factoryName="Python" temporary="true" nameIsGenerated="true">
+      <module name="dylab" />
+      <option name="INTERPRETER_OPTIONS" value="" />
+      <option name="PARENT_ENVS" value="true" />
+      <envs>
+        <env name="PYTHONUNBUFFERED" value="1" />
+      </envs>
+      <option name="SDK_HOME" value="" />
+      <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$" />
+      <option name="IS_MODULE_SDK" value="true" />
+      <option name="ADD_CONTENT_ROOTS" value="true" />
+      <option name="ADD_SOURCE_ROOTS" value="true" />
+      <EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" />
+      <option name="SCRIPT_NAME" value="$PROJECT_DIR$/test.py" />
       <option name="PARAMETERS" value="" />
       <option name="SHOW_COMMAND_LINE" value="false" />
       <option name="EMULATE_TERMINAL" value="false" />
@@ -155,9 +167,10 @@
     </configuration>
     <recent_temporary>
       <list>
+        <item itemvalue="Python.test (1)" />
         <item itemvalue="Python.test_living_plot" />
         <item itemvalue="Python.test" />
-        <item itemvalue="Python.Plotting" />
+        <item itemvalue="Python.Plotting1" />
         <item itemvalue="Python.test_fitting" />
       </list>
     </recent_temporary>
@@ -177,7 +190,7 @@
       <workItem from="1658844297242" duration="39201000" />
       <workItem from="1659027245256" duration="8511000" />
       <workItem from="1659078820495" duration="69000" />
-      <workItem from="1659078901335" duration="36607000" />
+      <workItem from="1659078901335" duration="89130000" />
     </task>
     <task id="LOCAL-00001" summary="First working version. Need introductions">
       <created>1658494877565</created>
@@ -200,7 +213,14 @@
       <option name="project" value="LOCAL" />
       <updated>1658822265357</updated>
     </task>
-    <option name="localTasksCounter" value="4" />
+    <task id="LOCAL-00004" summary="Update for plotting function.">
+      <created>1659210654086</created>
+      <option name="number" value="00004" />
+      <option name="presentableId" value="LOCAL-00004" />
+      <option name="project" value="LOCAL" />
+      <updated>1659210654086</updated>
+    </task>
+    <option name="localTasksCounter" value="5" />
     <servers />
   </component>
   <component name="TypeScriptGeneratedFilesManager">
@@ -222,7 +242,8 @@
     <MESSAGE value="First working version. Need introductions" />
     <MESSAGE value="Debug for calculating atom number.&#10;&#10;Add selecting the effective area function in AbsorptionImaging.py.&#10;&#10;Optimaze plotting function." />
     <MESSAGE value="Debug for calculating atom number.&#10;&#10;Add background subtraction function.&#10;&#10;Correct the pixel size of the camera" />
-    <option name="LAST_COMMIT_MESSAGE" value="Debug for calculating atom number.&#10;&#10;Add background subtraction function.&#10;&#10;Correct the pixel size of the camera" />
+    <MESSAGE value="Update for plotting function." />
+    <option name="LAST_COMMIT_MESSAGE" value="Update for plotting function." />
   </component>
   <component name="XDebuggerManager">
     <breakpoint-manager>
@@ -247,6 +268,10 @@
           <line>7</line>
           <option name="timeStamp" value="57" />
         </line-breakpoint>
+        <line-breakpoint enabled="true" suspend="THREAD" type="python-line">
+          <url>file://$PROJECT_DIR$/HelperClasses/Plotting1.py</url>
+          <option name="timeStamp" value="61" />
+        </line-breakpoint>
       </breakpoints>
       <default-breakpoints>
         <breakpoint type="python-exception">
@@ -259,6 +284,7 @@
   </component>
   <component name="com.intellij.coverage.CoverageDataManagerImpl">
     <SUITE FILE_PATH="coverage/dylab$test_living_plot.coverage" NAME="test_living_plot Coverage Results" MODIFIED="1659127460208" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" />
+    <SUITE FILE_PATH="coverage/dylab$test__1_.coverage" NAME="test (1) Coverage Results" MODIFIED="1659948939920" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" />
     <SUITE FILE_PATH="coverage/dylab$Plotting.coverage" NAME="Plotting Coverage Results" MODIFIED="1659081506380" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$/HelperClasses" />
     <SUITE FILE_PATH="coverage/dylab$test_fitting.coverage" NAME="test_fitting Coverage Results" MODIFIED="1658416885056" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" />
     <SUITE FILE_PATH="coverage/dylab$test.coverage" NAME="test Coverage Results" MODIFIED="1659126746245" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$/HelperClasses" />
diff --git a/HelperClasses/AbsorptionImaging.py b/HelperClasses/AbsorptionImaging.py
index ff6e45d..50a96e7 100644
--- a/HelperClasses/AbsorptionImaging.py
+++ b/HelperClasses/AbsorptionImaging.py
@@ -40,7 +40,8 @@ class absorption_imaging:
         # Ideally, we should be able to access all the data by function data(path).
         # However it is still under development. Now we can not read a picture by using function data(path).
         # We have to change to use function Run(path), which creat a class with the saved hdf5 file.
-        self.data_handle = Run(data_path)
+        if data_path is not None:
+            self.data_handle = Run(data_path)
 
         # Path of the saving images
         self.camera_orientation = camera_orientation
@@ -130,8 +131,8 @@ class absorption_imaging:
 
         self.x_start = left_up_conner[0]
         self.x_end = right_down_conner[0]
-        self.y_start = left_up_conner[1]
-        self.y_end = right_down_conner[1]
+        self.y_end = left_up_conner[1]
+        self.y_start = right_down_conner[1]
 
         self.image_absorption_cut = self.image_absorption[self.y_start:self.y_end, self.x_start:self.x_end]
 
diff --git a/HelperClasses/Plotting/DataExtractorLyse.py b/HelperClasses/Plotting/DataExtractorLyse.py
index 58228b7..d3f0ff3 100644
--- a/HelperClasses/Plotting/DataExtractorLyse.py
+++ b/HelperClasses/Plotting/DataExtractorLyse.py
@@ -92,14 +92,26 @@ class DataExtractor:
 
         elif self.data_type == 'single':
             try:
-                if len(self.data_path) == 1:
-                    result = data_handle.get_globals(self.data_path[0], h5_file=h5_file)
-                else:
                     result = data_handle.get_result(self.data_path[0], self.data_path[1],
                                                     h5_file=h5_file)
             except:
                 result = None
 
+        elif self.data_type == 'global':
+            try:
+                    result = data_handle.get_globals(self.data_path[0], h5_file=h5_file)
+                    result = result[self.data_path[1]]
+            except:
+                result = None
+
+        elif self.data_type == 'image':
+            try:
+                result = data_handle.get_image(self.data_path[0], self.data_path[1],
+                                               self.data_path[2], h5_file=h5_file)
+                result = np.array(result)
+            except:
+                result = None
+
         return result
 
     def update_local_data(self, h5_path, h5_file=None):
diff --git a/HelperClasses/Plotting/MainPlotPanel.py b/HelperClasses/Plotting/MainPlotPanel.py
index 874e5f3..d47caf8 100644
--- a/HelperClasses/Plotting/MainPlotPanel.py
+++ b/HelperClasses/Plotting/MainPlotPanel.py
@@ -6,7 +6,8 @@ from pyqtgraph.dockarea import *
 from PyQt5.QtWidgets import *
 from PyQt5.QtCore import *
 import lyse
-from .WidgetDataSelector import ShotSelector
+from .WidgetDataSelector import WidgetDataSelector
+from .WidgetAnalysePanel import WidgetAnalysePanel
 
 
 class MainPlotPanel(QtGui.QMainWindow):
@@ -25,19 +26,25 @@ class MainPlotPanel(QtGui.QMainWindow):
         self.area = DockArea()
 
         self.setCentralWidget(self.area)
-        self.resize(1000, 500)
+        self.resize(900, 500)
 
         self.dshotselector = Dock("Shot selector")
-        self.shotselector = ShotSelector()
+        self.shotselector = WidgetDataSelector()
+        self.dshotselector.setFixedSize(400, 150)
 
         self.dshotselector.addWidget(self.shotselector)
-        self.area.addDock(self.dshotselector, 'bottom')
+        self.area.addDock(self.dshotselector, 'left')
 
         # self.qpg_dock = Dock("Quick Plot Generator")
         # self.qpg_dock.addWidget(QuickPlotGenerator(self))
         # self.qpg_dock.setMinimumSize(self.qpg_dock.minimumSizeHint())
         # self.area.addDock(self.qpg_dock)
 
+        self.danalyse_panel = Dock("Analyse and Fitting")
+        self.analyse_panel = WidgetAnalysePanel()
+        self.danalyse_panel.addWidget(self.analyse_panel)
+        self.area.addDock(self.danalyse_panel, 'bottom')
+
         self.show()
 
         self.plots = {}
@@ -47,7 +54,7 @@ class MainPlotPanel(QtGui.QMainWindow):
 
         self.df = lyse.data()
 
-    def add_plot_dock(self, plot_name, plot_widget, **kwargs):
+    def add_plot_dock(self, plot_name, plot_widget, overlap=True, **kwargs):
         if plot_name not in self.plots:
             plot_widget.plot_name = plot_name
 
@@ -55,7 +62,9 @@ class MainPlotPanel(QtGui.QMainWindow):
 
             dock.sigClosed.connect(self.remove_plot)
             dock.addWidget(plot_widget)
-            if len(self.plots):
+            if overlap and len(self.plots):
+                self.area.addDock(dock, 'above', relativeTo=self.area.docks[list(self.plots.keys())[-1]])
+            elif len(self.plots):
                 if len(self.plots) % self.n_rows == 2:
                     position = 'right'
                     self.area.addDock(dock, position)
diff --git a/HelperClasses/Plotting/WidgetAnalysePanel.py b/HelperClasses/Plotting/WidgetAnalysePanel.py
new file mode 100644
index 0000000..8e0b84c
--- /dev/null
+++ b/HelperClasses/Plotting/WidgetAnalysePanel.py
@@ -0,0 +1,86 @@
+import pyqtgraph as pg
+from pyqtgraph import Qt
+from pyqtgraph.Qt import QtCore, QtGui
+from PyQt5.QtWidgets import *
+from PyQt5.QtCore import *
+
+from .DataExtractorLyse import DataExtractorManager
+
+
+class WidgetAnalysePanel(QSplitter):
+    def __init__(self, **kwargs):
+
+        super().__init__(**kwargs)
+
+        self.setOrientation(Qt.Vertical)
+
+        # Add title
+        self.title = QtGui.QLabel()
+        self.title.setAlignment(QtCore.Qt.AlignCenter)
+        self.title.setText('<h2>' + 'Analyse and Fitting' + ' <\h2>')
+        self.title.setFixedHeight(30)
+        self.addWidget(self.title)
+
+        self.bottom = QSplitter()
+        self.addWidget(self.bottom)
+
+        self.absorption_image = None
+        self.absorption_image_plot = None
+        self.absorption_image_atom_number = None
+
+    def update_absorption_imaging_atom_number(self):
+        x, y = self.absorption_image_plot.roi.pos()
+        x_span, y_span = self.absorption_image_plot.roi.size()
+
+        x = int(x)
+        y = int(y)
+        x_span = int(x_span)
+        y_span = int(y_span)
+
+        left_up_conner = (x, y + y_span)
+        right_down_conner = (x + x_span, y)
+
+        self.absorption_image.image_absorption = self.absorption_image_plot.data_image
+
+        self.absorption_image.select_effective_data(left_up_conner, right_down_conner)
+
+        self.absorption_image.get_atom_number(force_to_run=True)
+
+        self.absorption_image_atom_number.setText(str(self.absorption_image.atom_number))
+
+    def add_absorption_imaging(self, absorption_image, widget_fake_color_plot):
+
+        self.absorption_image = absorption_image
+        self.absorption_image_plot = widget_fake_color_plot
+        self.absorption_image.image_absorption = self.absorption_image_plot.data_image
+
+        self.absorption_image_plot.roi.sigRegionChanged.connect(self.update_absorption_imaging_atom_number)
+        self.absorption_image_plot.analyse_panel_update = self.update_absorption_imaging_atom_number
+
+        current_box = QSplitter()
+        current_box.setOrientation(Qt.Vertical)
+
+        title = QLabel('Absorption Imaging')
+        title.setAlignment(Qt.AlignCenter)
+        title.setFixedHeight(30)
+        current_box.addWidget(title)
+
+        atom_number_box = QSplitter()
+        atom_number_box.setOrientation(Qt.Horizontal)
+        atom_number_title = QLabel('  Atom Number: ')
+        atom_number_title.setAlignment(Qt.AlignCenter)
+        self.absorption_image_atom_number = QLineEdit()
+        self.absorption_image_atom_number.setText(str(absorption_image.atom_number))
+        self.absorption_image_atom_number.setReadOnly(True)
+        atom_number_title.setFixedHeight(30)
+        self.absorption_image_atom_number.setFixedHeight(30)
+        atom_number_box.addWidget(atom_number_title)
+        atom_number_box.addWidget(self.absorption_image_atom_number)
+        current_box.addWidget(atom_number_box)
+
+        next_box = QSplitter()
+        next_box.addWidget(current_box)
+        self.bottom.addWidget(next_box)
+        self.bottom = next_box
+
+
diff --git a/HelperClasses/Plotting/WidgetDataSelector.py b/HelperClasses/Plotting/WidgetDataSelector.py
index 2b65830..a150366 100644
--- a/HelperClasses/Plotting/WidgetDataSelector.py
+++ b/HelperClasses/Plotting/WidgetDataSelector.py
@@ -9,7 +9,7 @@ from sortedcontainers import SortedSet
 
 
 # ShotSelector class for choosing which the hdf5 files are import for plotting
-class ShotSelector(pg.LayoutWidget):
+class WidgetDataSelector(pg.LayoutWidget):
     valueChanged = pyqtSignal()
     selectionChanged = pyqtSignal()
 
diff --git a/HelperClasses/Plotting/WidgetFakeColorPlot.py b/HelperClasses/Plotting/WidgetFakeColorPlot.py
index cc7b4a7..bc6d67c 100644
--- a/HelperClasses/Plotting/WidgetFakeColorPlot.py
+++ b/HelperClasses/Plotting/WidgetFakeColorPlot.py
@@ -1,16 +1,19 @@
-import pyqtgraph as pg
-from pyqtgraph import Qt
-from pyqtgraph.Qt import QtCore, QtGui
 import numpy as np
-
-from pyqtgraph.dockarea import *
-from PyQt5.QtWidgets import *
-from PyQt5.QtCore import *
+from PyQt5 import QtGui
+from PyQt5.QtGui import QDoubleValidator
 
 from .DataExtractorLyse import DataExtractorManager
-# import DataExtractorLyse
-from .WidgetPlot import DataPlot
-# import WidgetPlot
+from .WidgetPlot import WidgetPlot
+
+import pyqtgraph as pg
+from pyqtgraph import OrderedDict
+from PyQt5.QtWidgets import QLabel, QLineEdit
+from pyqtgraph import Qt
+from pyqtgraph.Qt import QtCore
+from PyQt5.QtWidgets import *
+from PyQt5.QtCore import *
+from PyQt5.QtGui import QRegExpValidator
+from PyQt5.QtCore import QRegExp
 
 from PIL import ImageColor
 
@@ -27,44 +30,135 @@ color_palette_html = ['#1f77b4',
 
 color_palette = [ImageColor.getcolor(color, "RGB") for color in color_palette_html]
 
+Gradients = OrderedDict([
+    ('bw', {'ticks': [(0.0, (0, 0, 0, 255)), (1, (255, 255, 255, 255))], 'mode': 'rgb'}),
+    ('hot', {'ticks': [(0.3333, (185, 0, 0, 255)), (0.6666, (255, 220, 0,
+                                                             255)), (1, (255, 255, 255, 255)), (0, (0, 0, 0, 255))],
+             'mode': 'rgb'}),
+    ('jet0', {'ticks': [(1, (166, 0, 0, 255)),
+                       (0.32247191011235954, (0, 255, 255, 255)),
+                       (0.11348314606741573, (0, 68, 255, 255)),
+                       (0.6797752808988764, (255, 255, 0, 255)),
+                       (0.902247191011236, (255, 0, 0, 255)),
+                       (0.5022471910112359, (0, 255, 0, 255)),
+                       (0.0, (0, 0, 166, 255))],
+             'mode': 'rgb'}),
+    ('jet', {'ticks': [(1, (128, 0, 0, 255)),
+                       (0.878431372549020, (255, 0, 0, 255)),
+                       (0.627450980392157, (255, 255, 0, 255)),
+                       (0.376470588235294, (0, 255, 255, 255)),
+                       (0.125490196078431, (0, 0, 255, 255)),
+                       (0.0, (0, 0, 131, 255))],
+             'mode': 'rgb'}),
+    ('summer', {'ticks': [(1, (255, 255, 0, 255)), (0.0, (0, 170, 127, 255))], 'mode': 'rgb'}),
+    ('space', {'ticks': [(0.562, (75, 215, 227, 255)), (0.087, (255, 170, 0, 254)), (0.332, (0, 255, 0, 255)),
+                         (0.77, (85, 0, 255, 255)), (0.0, (255, 0, 0, 255)), (1.0, (255, 0, 127, 255))],
+               'mode': 'rgb'}),
+    ('winter', {'ticks': [(1, (0, 255, 127, 255)), (0.0, (0, 0, 255, 255))], 'mode': 'rgb'})
+])
 
-class FakeColorPlot(DataPlot):
-    def __init__(self, title, data_path=None, **kwargs):
+
+class WidgetFakeColorPlot(WidgetPlot):
+    def __init__(self, title, data_path=None, data_group=None, Isocurve=False, Roi=True, HistogramLUT=False, colorbarText=True, **kwargs):
 
         super().__init__(title, **kwargs)
 
+        self.colorbarText = colorbarText
+
+        self.analyse_panel_update = None
+
         # set data extractor
-        self.data_extractor_manager = DataExtractorManager(data_path)
-        self.data_extractor_manager.add_data_extractor('data_img', 'array', data_path)
-        self.data_extractor_manager.add_data_extractor('x', 'array', (data_path[0], 'x'))
-        self.data_extractor_manager.add_data_extractor('y', 'array', (data_path[0], 'y'))
-        self.data_extractor_manager.add_data_extractor('warning', 'single', (data_path[0], 'warning'))
+        if data_group is None or data_group == 'results':
+            self.data_extractor_manager = DataExtractorManager(data_path)
+            self.data_extractor_manager.add_data_extractor('data_img', 'array', data_path)
+            self.data_extractor_manager.add_data_extractor('x', 'array', (data_path[0], 'x'))
+            self.data_extractor_manager.add_data_extractor('y', 'array', (data_path[0], 'y'))
+            self.data_extractor_manager.add_data_extractor('warning', 'single', (data_path[0], 'warning'))
+        else:
+            self.data_extractor_manager = DataExtractorManager(data_path)
+            self.data_extractor_manager.add_data_extractor('data_img', 'image', (data_group, data_path[0], data_path[1]))
+
+        self.data_image = None
 
         self.setMinimumHeight(550)
         self.setMinimumWidth(550)
 
+        if Roi is True:
+            # Add y-axis data slider
+            self.axsumy = self.plots.addPlot(title="")
+            self.axsumy.setFixedWidth(300)
+            self.sumy = self.axsumy.plot()
+            self.sumy_data = self.axsumy.plot(pen=pg.mkPen(style=QtCore.Qt.DashLine, color=color_palette[1]))
+
         # Add imaging
-        self.img = pg.ImageItem()
         self.aximg = self.plots.addPlot(title="")
+        self.img = pg.ImageItem()
         self.aximg.addItem(self.img)
 
-        # Isocurve draplotsg
-        self.iso = pg.IsocurveItem(level=1000, pen=color_palette[2])
-        self.iso.setParentItem(self.img)
-        self.iso.setZValue(5)
+        # fixe the y-axis
+        if Roi is True:
+            self.axsumy.setYLink(self.aximg)
 
         # Contrast/color control
-        self.hist = pg.HistogramLUTItem()
-        self.hist.setImageItem(self.img)
-        self.plots.addItem(self.hist)
+        self.colorbar = None
+        if HistogramLUT is True:
+            self.colorbar = pg.HistogramLUTItem()
+            self.colorbar.setImageItem(self.img)
+            self.colormap = Gradients['jet']
+            self.colorbar.gradient.restoreState(self.colormap)
+            self.plots.addItem(self.colorbar)
+        else:
+            colormap = pg.colormap.getFromMatplotlib('jet')
+            self.colorbar = pg.ColorBarItem(cmap=colormap, values=(0, 1))
+            self.colorbar.setImageItem(self.img, insert_in=self.aximg)
 
-        # Draggable line for setting isocurve level
-        self.isoLine = pg.InfiniteLine(angle=0, movable=True, pen=color_palette[2])
-        self.hist.vb.addItem(self.isoLine)
-        self.hist.vb.setMouseEnabled(y=False)  # makes user interaction a little easier
-        self.isoLine.setValue(1000)
-        self.isoLine.setZValue(1000)  # bring iso line above contrast controls
-        self.isoLine.sigDragged.connect(self.updateIsocurve)
+        self.iso = None
+        self.roi = None
+
+        if Isocurve is True:
+            # Isocurve draplotsg
+            self.iso = pg.IsocurveItem(level=0, pen=color_palette[2])
+            self.iso.setParentItem(self.img)
+            self.iso.setZValue(5)
+
+            # Draggable line for setting isocurve level
+            self.isoLine = pg.InfiniteLine(angle=0, movable=True, pen=color_palette[2])
+            self.colorbar.vb.addItem(self.isoLine)
+            self.colorbar.vb.setMouseEnabled(y=False)  # makes user interaction a little easier
+            self.isoLine.setValue(1000)
+            self.isoLine.setZValue(1000)  # bring iso line above contrast controls
+            self.isoLine.sigDragged.connect(self.updateIsocurve)
+
+        self.plots.nextRow()
+
+        if Roi is True:
+            # Custom ROI for selecting an image region
+            self.roi = pg.ROI([500, 500], [300, 300], pen={'color': 'k', 'width': 4})
+
+            self.roi.addScaleHandle([1, 0], [0.5, 0.5])
+            self.roi.addScaleHandle([0, 1], [0.5, 0.5])
+
+            self.aximg.addItem(self.roi)
+            self.roi.setZValue(10)  # make sure ROI is drawn above image
+            self.roi_ax = self.plots.addPlot()
+            self.roi_ax.setFixedHeight(300)
+            self.roi_ax.setFixedWidth(300)
+
+            self.roi_img = pg.ImageItem()
+            self.roi_ax.addItem(self.roi_img)
+
+            roi_colormap = pg.colormap.getFromMatplotlib('jet')
+            self.roi_img.setColorMap(roi_colormap)
+
+            self.roi.sigRegionChanged.connect(self.updateROI)
+            self.colorbar.sigLevelsChanged.connect(self.updateROI)
+
+            # Add x-axis data slider
+            self.axsumx = self.plots.addPlot()
+            self.axsumx.setFixedHeight(300)
+            self.axsumx.setXLink(self.aximg)
+            self.sumx = self.axsumx.plot()
+            self.sumx_data = self.axsumx.plot(pen=pg.mkPen(style=QtCore.Qt.DashLine, color=color_palette[1]))
 
         # Monkey-patch the image to use our custom hover function.
         # This is generally discouraged (you should subclass ImageItem instead),
@@ -81,25 +175,169 @@ class FakeColorPlot(DataPlot):
         self.cx = 0
         self.cy = 0
 
-        self.data_image = None
+        #Add text box for colorbar and ROI
+        self.colorbar_ROI_box = QSplitter()
+        self.colorbar_ROI_box.setOrientation(Qt.Horizontal)
+
+        if colorbarText is True:
+            # Add text box for colorbar
+            self.colorbar_box = QSplitter()
+            self.colorbar_box.setOrientation(Qt.Vertical)
+
+            self.colorbar_title = QLabel('Color Bar')
+            self.colorbar_title.setAlignment(Qt.AlignCenter)
+
+            self.colorbar_box_container = QSplitter()
+            self.colorbar_box_container.setOrientation(Qt.Horizontal)
+
+            self.colorbar_box_max_label = QLabel('  Max: ')
+            self.colorbar_box_max_label.setAlignment(Qt.AlignCenter)
+            self.colorbar_box_max_line = QLineEdit(self)
+            double_regex = QRegExp("^[-+0-9.]+$")
+            double_validator = QRegExpValidator(double_regex, self.colorbar_box_max_line)
+            self.colorbar_box_max_line.setValidator(double_validator)
+            self.colorbar_box_max_line.setAlignment(Qt.AlignLeft)
+
+            self.colorbar_box_min_label = QLabel('  Min: ')
+            self.colorbar_box_min_label.setAlignment(Qt.AlignCenter)
+            self.colorbar_box_min_line = QLineEdit(self)
+            double_regex = QRegExp("^[-+0-9.]+$")
+            double_validator = QRegExpValidator(double_regex, self.colorbar_box_min_line)
+            self.colorbar_box_min_line.setValidator(double_validator)
+            self.colorbar_box_min_line.setAlignment(Qt.AlignLeft)
+
+            self.colorbar_box_label = QSplitter()
+            self.colorbar_box_label.setOrientation(Qt.Vertical)
+            self.colorbar_box_line = QSplitter()
+            self.colorbar_box_line.setOrientation(Qt.Vertical)
+            self.colorbar_box_label.addWidget(self.colorbar_box_max_label)
+            self.colorbar_box_label.addWidget(self.colorbar_box_min_label)
+            self.colorbar_box_line.addWidget(self.colorbar_box_max_line)
+            self.colorbar_box_line.addWidget(self.colorbar_box_min_line)
+
+            self.colorbar_box_container.addWidget(self.colorbar_box_label)
+            self.colorbar_box_container.addWidget(self.colorbar_box_line)
+
+            self.colorbar_box.addWidget(self.colorbar_title)
+            self.colorbar_box.addWidget(self.colorbar_box_container)
+
+            self.colorbar_box_max_line.editingFinished.connect(self.update_colorbar_text)
+            self.colorbar_box_min_line.editingFinished.connect(self.update_colorbar_text)
+
+        if Roi is True:
+            #Add text box for ROI
+            self.roi_box = QSplitter()
+            self.roi_box.setOrientation(Qt.Vertical)
+
+            self.roi_box_title = QLabel('Region of Interest')
+            self.roi_box_title.setAlignment(Qt.AlignCenter)
+
+            self.roi_box_container = QSplitter()
+            self.roi_box_container.setOrientation(Qt.Horizontal)
+            self.roi_center_container = QSplitter()
+            self.roi_center_container.setOrientation(Qt.Horizontal)
+            self.roi_span_container = QSplitter()
+            self.roi_span_container.setOrientation(Qt.Horizontal)
+
+            self.roi_center_label = QSplitter()
+            self.roi_center_label.setOrientation(Qt.Vertical)
+            self.roi_center_line = QSplitter()
+            self.roi_center_line.setOrientation(Qt.Vertical)
+
+            self.roi_span_label = QSplitter()
+            self.roi_span_label.setOrientation(Qt.Vertical)
+            self.roi_span_line = QSplitter()
+            self.roi_span_line.setOrientation(Qt.Vertical)
+
+            self.roi_center_x_label = QLabel('  X: ')
+            self.roi_center_x_label.setAlignment(Qt.AlignCenter)
+            self.roi_center_x_line = QLineEdit(self)
+            double_regex = QRegExp("^[-+0-9.]+$")
+            double_validator = QRegExpValidator(double_regex, self.roi_center_x_line)
+            self.roi_center_x_line.setValidator(double_validator)
+            self.roi_center_x_line.setAlignment(Qt.AlignLeft)
+
+            self.roi_center_y_label = QLabel('  Y: ')
+            self.roi_center_y_label.setAlignment(Qt.AlignCenter)
+            self.roi_center_y_line = QLineEdit(self)
+            double_regex = QRegExp("^[-+0-9.]+$")
+            double_validator = QRegExpValidator(double_regex, self.roi_center_y_line)
+            self.roi_center_y_line.setValidator(double_validator)
+            self.roi_center_y_line.setAlignment(Qt.AlignLeft)
+
+            self.roi_span_x_label = QLabel('  X Span: ')
+            self.roi_span_x_label.setAlignment(Qt.AlignCenter)
+            self.roi_span_x_line = QLineEdit(self)
+            double_regex = QRegExp("^[-+0-9.]+$")
+            double_validator = QRegExpValidator(double_regex, self.roi_span_x_line)
+            self.roi_span_x_line.setValidator(double_validator)
+            self.roi_span_x_line.setAlignment(Qt.AlignLeft)
+
+            self.roi_span_y_label = QLabel('  Y Span: ')
+            self.roi_span_y_label.setAlignment(Qt.AlignCenter)
+            self.roi_span_y_line = QLineEdit(self)
+            double_regex = QRegExp("^[-+0-9.]+$")
+            double_validator = QRegExpValidator(double_regex, self.roi_span_y_line)
+            self.roi_span_y_line.setValidator(double_validator)
+            self.roi_span_y_line.setAlignment(Qt.AlignLeft)
+
+            self.roi_center_label.addWidget(self.roi_center_x_label)
+            self.roi_center_label.addWidget(self.roi_center_y_label)
+            self.roi_center_line.addWidget(self.roi_center_x_line)
+            self.roi_center_line.addWidget(self.roi_center_y_line)
+            self.roi_span_label.addWidget(self.roi_span_x_label)
+            self.roi_span_label.addWidget(self.roi_span_y_label)
+            self.roi_span_line.addWidget(self.roi_span_x_line)
+            self.roi_span_line.addWidget(self.roi_span_y_line)
+
+            self.roi_center_container.addWidget(self.roi_center_label)
+            self.roi_center_container.addWidget(self.roi_center_line)
+            self.roi_span_container.addWidget(self.roi_span_label)
+            self.roi_span_container.addWidget(self.roi_span_line)
+
+            self.roi_box_container.addWidget(self.roi_center_container)
+            self.roi_box_container.addWidget(self.roi_span_container)
+            self.roi_box.addWidget(self.roi_box_title)
+            self.roi_box.addWidget(self.roi_box_container)
+
+            self.roi_center_x_line.editingFinished.connect(self.updateROI_text)
+            self.roi_center_y_line.editingFinished.connect(self.updateROI_text)
+            self.roi_span_x_line.editingFinished.connect(self.updateROI_text)
+            self.roi_span_y_line.editingFinished.connect(self.updateROI_text)
+
+            self.colorbar_ROI_box.addWidget(self.colorbar_box)
+            self.colorbar_ROI_box.addWidget(self.roi_box)
+
+        self.bottom.addWidget(self.colorbar_ROI_box)
 
     def update(self, h5_path):
 
         data = self.data_extractor_manager.get_data(h5_path)
-        data_img = data['data_img']
-        x = data['x']
-        y = data['y']
+        self.data_image = data['data_img']
+
+        try:
+            x = data['x']
+            y = data['y']
+            warning = data['warning']
+        except:
+            x = None
+            y = None
+            warning = None
+
         if x is None:
-            x = np.linspace(0, data_img.shape[0], data_img.shape[0])
+            x = np.linspace(0, self.data_image.shape[0], self.data_image.shape[0])
         if y is None:
-            y = np.linspace(0, data_img.shape[1], data_img.shape[1])
-        warning = data['warning']
+            y = np.linspace(0, self.data_image.shape[1], self.data_image.shape[1])
 
         # update plots
-        self.img.setImage(data_img.T)
-        self.iso.setData(data_img.T)
+        if self.colorbarText is True:
+            self.img.setImage(self.data_image.T, autoLevels=False)
+        else:
+            self.img.setImage(self.data_image.T, autoLevels=True)
+            self.colorbar.setLevels((np.min(self.data_image), np.max(self.data_image)))
 
-        self.data_img = data_img
+        if self.iso is not None:
+            self.iso.setData(self.data_image.T)
 
         # set position and scale of image
         newscalex = x[1] - x[0]
@@ -117,12 +355,72 @@ class FakeColorPlot(DataPlot):
         self.cx = x[0]
         self.cy = y[0]
 
+        # update the region of interest
+        if self.roi is not None:
+            self.updateROI()
+
         # update table and warning
         self.update_warning(warning)
 
+        if self.analyse_panel_update is not None:
+            self.analyse_panel_update()
+
     def updateIsocurve(self):
         self.iso.setLevel(self.isoLine.value())
 
+    def update_colorbar_text(self):
+        colorbar_max = self.colorbar_box_max_line.text()
+        colorbar_min = self.colorbar_box_min_line.text()
+        colorbar_max = float(colorbar_max)
+        colorbar_min = float(colorbar_min)
+        try:
+            self.colorbar.setLevels(min=colorbar_min, max=colorbar_max)
+        except:
+            self.colorbar.setLevels(low=colorbar_min, high=colorbar_max)
+        if self.roi is not None:
+            self.updateROI()
+
+    def updateROI(self):
+        selected = self.roi.getArrayRegion(self.data_image.T, self.img)
+        try:
+            levels = self.colorbar.getLevels()
+        except:
+            levels = self.colorbar.levels()
+        self.roi_img.setImage(selected, levels=levels)
+
+        colorbar_min, colorbar_max = levels
+        self.colorbar_box_max_line.setText(str(colorbar_max))
+        self.colorbar_box_min_line.setText(str(colorbar_min))
+
+        x_center, y_center = self.roi.pos()
+        x_span, y_span = self.roi.size()
+        x_center = x_center + x_span / 2
+        y_center = y_center + y_span / 2
+        self.roi_center_x_line.setText(str(x_center))
+        self.roi_center_y_line.setText(str(y_center))
+        self.roi_span_x_line.setText(str(x_span))
+        self.roi_span_y_line.setText(str(y_span))
+
+        roi_pos = self.roi.pos()
+
+        pos = int(selected.shape[0]/2)
+        x = np.linspace(roi_pos[1], roi_pos[1] + selected.shape[1], selected.shape[1])
+        self.sumy_data.setData(x=np.squeeze(selected[pos:pos+1, :]), y=x)
+
+        pos = int(selected.shape[1] / 2)
+        x = np.linspace(roi_pos[0], roi_pos[0] + selected.shape[0], selected.shape[0])
+        self.sumx_data.setData(x=x, y=np.squeeze(selected[:, pos:pos + 1]))
+
+    def updateROI_text(self):
+        x_center = float(self.roi_center_x_line.text())
+        y_center = float(self.roi_center_y_line.text())
+        x_span = float(self.roi_span_x_line.text())
+        y_span = float(self.roi_span_y_line.text())
+        x = x_center - x_span / 2
+        y = y_center - y_span / 2
+        self.roi.setPos((x, y))
+        self.roi.setSize((x_span, y_span))
+
     def imageHoverEvent(self, event):
         """Show the position, pixel, and value under the mouse cursor.
         """
@@ -131,9 +429,9 @@ class FakeColorPlot(DataPlot):
             return
         pos = event.pos()
         i, j = pos.y(), pos.x()
-        i = int(np.clip(i, 0, self.data_img.shape[0] - 1))
-        j = int(np.clip(j, 0, self.data_img.shape[1] - 1))
-        val = self.data_img[i, j]
+        i = int(np.clip(i, 0, self.data_image.shape[0] - 1))
+        j = int(np.clip(j, 0, self.data_image.shape[1] - 1))
+        val = self.data_image[i, j]
         ppos = self.img.mapToParent(pos)
         x, y = ppos.x(), ppos.y()
-        self.aximg.setTitle("pos: (%0.1f, %0.1f) value: %g" % (x, y, val))
\ No newline at end of file
+        self.aximg.setTitle("pos: (%0.1f, %0.1f) value: %g" % (x, y, val))
diff --git a/HelperClasses/Plotting/WidgetPlot.py b/HelperClasses/Plotting/WidgetPlot.py
index 49a073e..646e608 100644
--- a/HelperClasses/Plotting/WidgetPlot.py
+++ b/HelperClasses/Plotting/WidgetPlot.py
@@ -7,39 +7,35 @@ from PyQt5.QtCore import *
 from .DataExtractorLyse import DataExtractorManager
 
 
-class DataPlot(QSplitter):
+class WidgetPlot(QSplitter):
     def __init__(self, title, **kwargs):
         super().__init__(**kwargs)
 
         # Orientation of plot and title (and other information)
         self.setOrientation(Qt.Vertical)
 
-        # Add plot
-        self.plots = pg.GraphicsLayoutWidget()
-        self.addWidget(self.plots)
-
-        # Claim bottom part (title)
-        self.bottom = QSplitter()
-        self.bottom.setOrientation(Qt.Horizontal)
-        self.addWidget(self.bottom)
-
         # Add title
         self.title = QtGui.QLabel()
         self.title.setAlignment(QtCore.Qt.AlignCenter)
         self.title.setText('<h2>' + title + ' <\h2>')
-        self.desciption = pg.LayoutWidget()
-        self.desciption.addWidget(self.title)
+        self.addWidget(self.title)
+
+        # Claim bottom part (title)
+        self.bottom = QSplitter()
+        self.bottom.setOrientation(Qt.Vertical)
+        self.addWidget(self.bottom)
+
+        # Add plot
+        self.plots = pg.GraphicsLayoutWidget()
+        self.bottom.addWidget(self.plots)
 
         # Add warning information
+        self.desciption = pg.LayoutWidget()
         self.warning = QtGui.QLabel()
         self.warning.setAlignment(QtCore.Qt.AlignCenter)
         self.desciption.nextRow()
         self.desciption.addWidget(self.warning)
-        self.bottom.addWidget(self.desciption)
-
-        # Add a table for fitting information
-        self.table = pg.TableWidget()
-        self.bottom.addWidget(self.table)
+        # self.bottom.addWidget(self.desciption)
 
         # Current hdf5 file path
         self.h5_path_shown = None
diff --git a/test.py b/test.py
index 66ba3fb..996fdac 100644
--- a/test.py
+++ b/test.py
@@ -1,13 +1,2 @@
-import lyse
-from pylab import *
-from lyse import *
-
-run = Run(path)
-
-imaging = 'absorption_imaging'
-cam = 'absorption_imaging'
-h5_paths = lyse.h5_paths()
-
-print(run.globals_groups())
-
-print(run.get_result_arrays(imaging, cam))
+import pyqtgraph.examples
+pyqtgraph.examples.run()
diff --git a/test_absorption_imaging.py b/test_absorption_imaging.py
index e262bc4..437c231 100644
--- a/test_absorption_imaging.py
+++ b/test_absorption_imaging.py
@@ -1,5 +1,5 @@
 from lyse import *
-from HelperClasses import DyTransition, Camera, AbsorptionImaging, Plotting
+from HelperClasses import DyTransition, Camera, AbsorptionImaging, Plotting1
 import matplotlib.pyplot as plt
 import matplotlib.style as mplstyle
 
@@ -20,7 +20,7 @@ with AbsorptionImaging.absorption_imaging(path, 'MOT_3D_Camera', 'in_situ_absorp
     print(absorption_image.atom_number)
 
 
-plotting = Plotting.plotting_absorption_imaging(absorption_image)
+plotting = Plotting1.plotting_absorption_imaging(absorption_image)
 plotting.four_plots()
 # plotting.absorption_plots()
 
diff --git a/test_living_plot.py b/test_living_plot.py
index 471464a..48c4b5b 100644
--- a/test_living_plot.py
+++ b/test_living_plot.py
@@ -8,6 +8,7 @@ import lyse
 import numpy as np
 
 from HelperClasses.Plotting import WidgetFakeColorPlot, MainPlotPanel
+from HelperClasses import DyTransition, Camera, AbsorptionImaging
 
 import cProfile
 import pstats
@@ -15,7 +16,7 @@ import pstats
 profile = cProfile.Profile()
 profile.enable()
 
-fm = lyse.figure_manager
+figure_manager = lyse.figure_manager
 
 h5_paths = lyse.h5_paths()
 
@@ -26,32 +27,52 @@ else:
     # If not, get the filepath of the last shot of the lyse DataFrame
     h5_path = lyse.h5_paths().iloc[-1]
 
-print(h5_path)
-
 if len(h5_paths):
     last_globals = run = lyse.Run(h5_paths.iloc[-1]).get_globals()
 
-if not hasattr(fm, 'ap'):
-    fm.ap = MainPlotPanel.MainPlotPanel(h5_paths)
+if not hasattr(figure_manager, 'ap'):
+    figure_manager.MainPlotPanel = MainPlotPanel.MainPlotPanel(h5_paths)
 
-# Imaging Methods
-imagings = ['absorption_imaging']
+# Add absorption imaging
+plot_name = '3D-MOT Absorption Imaging - With Atoms'
+if not plot_name in figure_manager.MainPlotPanel.plots:
+    current_plotting = WidgetFakeColorPlot.WidgetFakeColorPlot(plot_name + '1', ('in_situ_absorption', 'atoms'),
+                                                               data_group='MOT_3D_Camera',
+                                                               Roi=False, colorbarText=False)
+    figure_manager.MainPlotPanel.add_plot_dock(plot_name + '1', current_plotting)
 
-cams = {'absorption_imaging': ['Cam_absorption']}
+plot_name = '3D-MOT Absorption Imaging - Without Atoms'
+if not plot_name in figure_manager.MainPlotPanel.plots:
+    current_plotting = WidgetFakeColorPlot.WidgetFakeColorPlot(plot_name + '1', ('in_situ_absorption', 'background'),
+                                                               data_group='MOT_3D_Camera',
+                                                               Roi=False, colorbarText=False)
+    figure_manager.MainPlotPanel.add_plot_dock(plot_name + '1', current_plotting)
 
-imaging = 'absorption_imaging'
-for cam in cams[imaging]:
-    plot_name = imaging + ' ' + cam
+plot_name = '3D-MOT Absorption Imaging - Dark'
+if not plot_name in figure_manager.MainPlotPanel.plots:
+    current_plotting = WidgetFakeColorPlot.WidgetFakeColorPlot(plot_name + '1', ('in_situ_absorption', 'dark'),
+                                                               data_group='MOT_3D_Camera',
+                                                               Roi=False, colorbarText=False)
+    figure_manager.MainPlotPanel.add_plot_dock(plot_name + '1', current_plotting)
 
-    if not plot_name in fm.ap.plots:
-        ip = WidgetFakeColorPlot.FakeColorPlot(plot_name, ('absorption_imaging', 'absorption_imaging'))
+plot_name = '3D-MOT Absorption Imaging'
+if not plot_name in figure_manager.MainPlotPanel.plots:
+    current_plotting = WidgetFakeColorPlot.WidgetFakeColorPlot(plot_name, ('absorption_imaging', 'absorption_imaging'))
 
-        fm.ap.add_plot_dock(plot_name, ip)
+    figure_manager.MainPlotPanel.add_plot_dock(plot_name, current_plotting)
 
-fm.ap.update_h5_paths(h5_paths)
-fm.ap.refresh(h5_path)
+    absorption_imaging_transition = DyTransition.creat_Dy421()
+    mot_3D_camera = Camera.c11440_36u(absorption_imaging_transition['wavelength'])
+    absorption_image = AbsorptionImaging.absorption_imaging(None, 'MOT_3D_Camera', 'in_situ_absorption',
+                                                                absorption_imaging_transition, mot_3D_camera, 0, 0)
+    figure_manager.MainPlotPanel.analyse_panel.add_absorption_imaging(absorption_image, current_plotting)
+
+figure_manager.MainPlotPanel.update_h5_paths(h5_paths)
+figure_manager.MainPlotPanel.refresh(h5_path)
 
 profile.disable()
 ps = pstats.Stats(profile)
 ps.sort_stats('cumtime')
 ps.print_stats(10)
+
+