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

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gao 2022-08-09 17:48:22 +02:00
parent 8760e48105
commit 98fd4f3ded
10 changed files with 120 additions and 39 deletions
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25
.idea/workspace.xml generated
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@ -2,15 +2,14 @@
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<change beforePath="$PROJECT_DIR$/HelperClasses/Plotting/WidgetDataSelector.py" beforeDir="false" afterPath="$PROJECT_DIR$/HelperClasses/Plotting/WidgetDataSelector.py" afterDir="false" />
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<change beforePath="$PROJECT_DIR$/test_living_plot.py" beforeDir="false" afterPath="$PROJECT_DIR$/test_living_plot.py" afterDir="false" />
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@ -190,7 +189,7 @@
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@ -220,7 +219,14 @@
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@ -272,6 +278,11 @@
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@ -284,7 +295,7 @@
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<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$" />
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10
HelperClasses/AbsorptionImaging.py
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@ -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_end = right_down_conner[0]
self.y_end = left_up_conner[1]
self.y_start = right_down_conner[1]
self.x_start = int(center[0] - span[0] / 2)
self.x_end = int(center[0] + span[0] / 2)
self.y_end = int(center[1] + span[1] / 2)
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]

2
HelperClasses/Plotting/DataExtractorLyse.py
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@ -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

3
HelperClasses/Plotting/MainPlotPanel.py
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@ -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 = {}

76
HelperClasses/Plotting/Widget1DLivingPlot.py Normal file
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@ -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

5
HelperClasses/Plotting/WidgetAnalysePanel.py
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@ -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)

2
HelperClasses/Plotting/WidgetFakeColorPlot.py
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@ -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

0
HelperClasses/Plotting/WidgetQuickWaterFlowPlot.py → HelperClasses/Plotting/WidgetQuickWaterFallPlot.py
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22
test_absorption_imaging.py
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@ -1,26 +1,16 @@
from lyse import *
from HelperClasses import DyTransition, Camera, AbsorptionImaging, Plotting1
import matplotlib.pyplot as plt
import matplotlib.style as mplstyle
import matplotlib
matplotlib.use("qt5agg")
mplstyle.use('fast')
from HelperClasses import DyTransition, Camera, AbsorptionImaging
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:
absorption_image.select_effective_data((800, 500), (1000, 700))
# Please selecte the effective area here
# 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)
plotting = Plotting1.plotting_absorption_imaging(absorption_image)
plotting.four_plots()
# plotting.absorption_plots()
# print(absorption_image.atom_number)

14
test_living_plot.py
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@ -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)
figure_manager.MainPlotPanel.refresh(h5_path)
# Add realtime plotting for atom number
# 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)