Update for 1D living plot, but exist a huge bug

.idea/workspace.xml

@@ -2,15 +2,14 @@
 <project version="4">
   <component name="ChangeListManager">
     <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 afterPath="$PROJECT_DIR$/HelperClasses/Plotting/Widget1DLivingPlot.py" afterDir="false" />
       <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" 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/WidgetAnalysePanel.py" beforeDir="false" afterPath="$PROJECT_DIR$/HelperClasses/Plotting/WidgetAnalysePanel.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="$PROJECT_DIR$/HelperClasses/Plotting/WidgetQuickWaterFlowPlot.py" beforeDir="false" afterPath="$PROJECT_DIR$/HelperClasses/Plotting/WidgetQuickWaterFallPlot.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_living_plot.py" beforeDir="false" afterPath="$PROJECT_DIR$/test_living_plot.py" afterDir="false" />
     </list>
@@ -190,7 +189,7 @@
       <workItem from="1658844297242" duration="39201000" />
       <workItem from="1659027245256" duration="8511000" />
       <workItem from="1659078820495" duration="69000" />
-      <workItem from="1659078901335" duration="89130000" />
+      <workItem from="1659078901335" duration="96964000" />
     </task>
     <task id="LOCAL-00001" summary="First working version. Need introductions">
       <created>1658494877565</created>
@@ -220,7 +219,14 @@
       <option name="project" value="LOCAL" />
       <updated>1659210654086</updated>
     </task>
-    <option name="localTasksCounter" value="5" />
+    <task id="LOCAL-00005" summary="Update for plotting function.">
+      <created>1660052254656</created>
+      <option name="number" value="00005" />
+      <option name="presentableId" value="LOCAL-00005" />
+      <option name="project" value="LOCAL" />
+      <updated>1660052254656</updated>
+    </task>
+    <option name="localTasksCounter" value="6" />
     <servers />
   </component>
   <component name="TypeScriptGeneratedFilesManager">
@@ -272,6 +278,11 @@
           <url>file://$PROJECT_DIR$/HelperClasses/Plotting1.py</url>
           <option name="timeStamp" value="61" />
         </line-breakpoint>
+        <line-breakpoint enabled="true" suspend="THREAD" type="python-line">
+          <url>file://$PROJECT_DIR$/../../../analysis_plot_panel/src/analysis_plot_panel/analysis_plot_panel_lyse_routine.py</url>
+          <line>6</line>
+          <option name="timeStamp" value="62" />
+        </line-breakpoint>
       </breakpoints>
       <default-breakpoints>
         <breakpoint type="python-exception">
@@ -284,7 +295,7 @@
   </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$test__1_.coverage" NAME="test (1) Coverage Results" MODIFIED="1660054001747" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="true" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$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" />

HelperClasses/AbsorptionImaging.py

@@ -127,12 +127,12 @@ class absorption_imaging:
 
     # select the effective data in an rectangle area defined by coordinates of two conner
     # The select region will be presented as a red box in the plotting
-    def select_effective_data(self, left_up_conner, right_down_conner):
+    def select_effective_data(self, center, span):
 
-        self.x_start = left_up_conner[0]
+        self.x_start = int(center[0] - span[0] / 2)
-        self.x_end = right_down_conner[0]
+        self.x_end = int(center[0] + span[0] / 2)
-        self.y_end = left_up_conner[1]
+        self.y_end = int(center[1] + span[1] / 2)
-        self.y_start = right_down_conner[1]
+        self.y_start = int(center[1] - span[1] / 2)
 
         self.image_absorption_cut = self.image_absorption[self.y_start:self.y_end, self.x_start:self.x_end]
 

HelperClasses/Plotting/DataExtractorLyse.py

@@ -23,7 +23,7 @@ class DataExtractorManager:
     def __init__(self, data_path=None):
 
         self.data_extractors = {}
-        self.h5_file = None
+        # self.h5_file = None
         self.data_path = data_path
         self.local_data_changed = False
 

HelperClasses/Plotting/MainPlotPanel.py

@@ -45,7 +45,8 @@ class MainPlotPanel(QtGui.QMainWindow):
         self.danalyse_panel.addWidget(self.analyse_panel)
         self.area.addDock(self.danalyse_panel, 'bottom')
 
-        self.show()
+        self.setWindowFlags(QtCore.Qt.WindowStaysOnTopHint)
+        self.showMaximized()
 
         self.plots = {}
 

HelperClasses/Plotting/Widget1DLivingPlot.py

@@ -0,0 +1,76 @@
+import numpy as np
+
+from .DataExtractorLyse import DataExtractorManager
+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
+
+
+class Widget1DLivingPlot(WidgetPlot):
+
+    def __init__(self, title, x_data_path=None, y_data_path=None, x_in_results=False, y_in_results=False, **kwargs):
+
+        super().__init__(title, **kwargs)
+
+        # set data extractor
+        if x_data_path is not None:
+            self.x_data_extractor_manager = DataExtractorManager(x_data_path)
+            self.x_data_extractor_manager.add_data_extractor('warning', 'single', (x_data_path[0], 'warning'))
+            if x_in_results:
+                self.x_data_extractor_manager.add_data_extractor('x', 'single', x_data_path)
+            else:
+                self.x_data_extractor_manager.add_data_extractor('x', 'global', x_data_path)
+        else:
+            self.x_data_extractor_manager = None
+
+        self.y_data_extractor_manager = DataExtractorManager(y_data_path)
+        self.y_data_extractor_manager.add_data_extractor('warning', 'single', (y_data_path[0], 'warning'))
+        if y_in_results:
+            self.y_data_extractor_manager.add_data_extractor('y', 'single', y_data_path)
+        else:
+            self.y_data_extractor_manager.add_data_extractor('y', 'global', y_data_path)
+
+        self.aximg = self.plots.addPlot(title="")
+        self.img = pg.PlotCurveItem()
+        self.aximg.setClipToView(True)
+        self.aximg.setDownsampling(mode='peak')
+        self.aximg.addItem(self.img)
+
+        self.x = np.empty(100)
+        self.y = np.empty(100)
+        self.current_data_length = 0
+
+    def update(self, h5_path):
+
+        if self.current_data_length >= self.x.shape[0]:
+            tmp = self.x
+            self.x = np.empty(self.x.shape[0] * 2)
+            self.x[:tmp.shape[0]] = tmp
+            tmp = self.y
+            self.y = np.empty(self.y.shape[0] * 2)
+            self.y[:tmp.shape[0]] = tmp
+
+        if self.x_data_extractor_manager is not None:
+            x_data = self.x_data_extractor_manager.get_data(h5_path)
+            self.x[self.current_data_length] = x_data['x']
+        else:
+            self.x[self.current_data_length] = self.current_data_length
+        y_data = self.y_data_extractor_manager.get_data(h5_path)
+        self.y[self.current_data_length] = y_data['y']
+
+        print(y_data['y'])
+        self.img.setData(x=self.x[:self.current_data_length], y=self.y[:self.current_data_length])
+        self.current_data_length = self.current_data_length + 1
+
+
+

HelperClasses/Plotting/WidgetAnalysePanel.py

@@ -37,12 +37,9 @@ class WidgetAnalysePanel(QSplitter):
         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.select_effective_data((x, y), (x_span, y_span))
 
         self.absorption_image.get_atom_number(force_to_run=True)
 

HelperClasses/Plotting/WidgetFakeColorPlot.py

@@ -1,6 +1,4 @@
 import numpy as np
-from PyQt5 import QtGui
-from PyQt5.QtGui import QDoubleValidator
 
 from .DataExtractorLyse import DataExtractorManager
 from .WidgetPlot import WidgetPlot

test_absorption_imaging.py

@@ -1,26 +1,16 @@
 from lyse import *
-from HelperClasses import DyTransition, Camera, AbsorptionImaging, Plotting1
+from HelperClasses import DyTransition, Camera, AbsorptionImaging
-import matplotlib.pyplot as plt
-import matplotlib.style as mplstyle
-
-import matplotlib
-matplotlib.use("qt5agg")
-
-mplstyle.use('fast')
 
 absorption_imaging_transition = DyTransition.creat_Dy421()
 mot_3D_camera = Camera.c11440_36u(absorption_imaging_transition['wavelength'])
 
 with AbsorptionImaging.absorption_imaging(path, 'MOT_3D_Camera', 'in_situ_absorption',
                                           absorption_imaging_transition, mot_3D_camera, 0, 0) as absorption_image:
-
+    # Please selecte the effective area here
-    absorption_image.select_effective_data((800, 500), (1000, 700))
+    # The first tuple is the center position (x,y)
+    # The second tuple is the span in x and y direction (x_span, y_span)
+    absorption_image.select_effective_data((900, 600), (200, 200))
     absorption_image.get_atom_number()
 
-    print(absorption_image.atom_number)
+    # print(absorption_image.atom_number)
-
-
-plotting = Plotting1.plotting_absorption_imaging(absorption_image)
-plotting.four_plots()
-# plotting.absorption_plots()
 

test_living_plot.py

@@ -7,7 +7,7 @@ Created on Thu Mar 11 14:58:18 2021
 import lyse
 import numpy as np
 
-from HelperClasses.Plotting import WidgetFakeColorPlot, MainPlotPanel
+from HelperClasses.Plotting import WidgetFakeColorPlot, MainPlotPanel, Widget1DLivingPlot
 from HelperClasses import DyTransition, Camera, AbsorptionImaging
 
 import cProfile
@@ -55,6 +55,7 @@ if not plot_name in figure_manager.MainPlotPanel.plots:
                                                                Roi=False, colorbarText=False)
     figure_manager.MainPlotPanel.add_plot_dock(plot_name + '1', current_plotting)
 
+# Add plotting for 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'))
@@ -67,8 +68,15 @@ if not plot_name in figure_manager.MainPlotPanel.plots:
                                                                 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)
+# Add realtime plotting for atom number
-figure_manager.MainPlotPanel.refresh(h5_path)
+# plot_name = '3D-MOT Atom Number'
+# if not plot_name in figure_manager.MainPlotPanel.plots:
+#     current_plotting = Widget1DLivingPlot.Widget1DLivingPlot(plot_name, y_data_path=('absorption_imaging', 'atom_number'), y_in_results=True)
+#
+#     figure_manager.MainPlotPanel.add_plot_dock(plot_name, current_plotting)
+#
+# figure_manager.MainPlotPanel.update_h5_paths(h5_paths)
+# figure_manager.MainPlotPanel.refresh(h5_path)
 
 profile.disable()
 ps = pstats.Stats(profile)