Update for plotting function.
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gao
parent
cb1c9637d2
commit
8760e48105
96
.idea/workspace.xml
generated
96
.idea/workspace.xml
generated
@ -1,36 +1,18 @@
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@ -64,8 +54,8 @@
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@ -78,7 +68,29 @@
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@ -222,7 +242,8 @@
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<MESSAGE value="Debug for calculating atom number. Add selecting the effective area function in AbsorptionImaging.py. Optimaze plotting function." />
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@ -40,7 +40,8 @@ class absorption_imaging:
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# Ideally, we should be able to access all the data by function data(path).
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# However it is still under development. Now we can not read a picture by using function data(path).
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# We have to change to use function Run(path), which creat a class with the saved hdf5 file.
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self.data_handle = Run(data_path)
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if data_path is not None:
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self.data_handle = Run(data_path)
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# Path of the saving images
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self.camera_orientation = camera_orientation
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@ -130,8 +131,8 @@ class absorption_imaging:
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self.x_start = left_up_conner[0]
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self.x_end = right_down_conner[0]
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self.y_start = left_up_conner[1]
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self.y_end = right_down_conner[1]
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self.y_end = left_up_conner[1]
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self.y_start = right_down_conner[1]
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self.image_absorption_cut = self.image_absorption[self.y_start:self.y_end, self.x_start:self.x_end]
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@ -92,14 +92,26 @@ class DataExtractor:
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elif self.data_type == 'single':
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try:
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if len(self.data_path) == 1:
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result = data_handle.get_globals(self.data_path[0], h5_file=h5_file)
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else:
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result = data_handle.get_result(self.data_path[0], self.data_path[1],
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h5_file=h5_file)
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except:
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result = None
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elif self.data_type == 'global':
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try:
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result = data_handle.get_globals(self.data_path[0], h5_file=h5_file)
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result = result[self.data_path[1]]
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except:
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result = None
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elif self.data_type == 'image':
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try:
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result = data_handle.get_image(self.data_path[0], self.data_path[1],
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self.data_path[2], h5_file=h5_file)
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result = np.array(result)
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except:
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result = None
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return result
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def update_local_data(self, h5_path, h5_file=None):
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@ -6,7 +6,8 @@ from pyqtgraph.dockarea import *
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from PyQt5.QtWidgets import *
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from PyQt5.QtCore import *
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import lyse
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from .WidgetDataSelector import ShotSelector
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from .WidgetDataSelector import WidgetDataSelector
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from .WidgetAnalysePanel import WidgetAnalysePanel
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class MainPlotPanel(QtGui.QMainWindow):
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@ -25,19 +26,25 @@ class MainPlotPanel(QtGui.QMainWindow):
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self.area = DockArea()
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self.setCentralWidget(self.area)
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self.resize(1000, 500)
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self.resize(900, 500)
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self.dshotselector = Dock("Shot selector")
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self.shotselector = ShotSelector()
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self.shotselector = WidgetDataSelector()
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self.dshotselector.setFixedSize(400, 150)
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self.dshotselector.addWidget(self.shotselector)
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self.area.addDock(self.dshotselector, 'bottom')
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self.area.addDock(self.dshotselector, 'left')
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# self.qpg_dock = Dock("Quick Plot Generator")
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# self.qpg_dock.addWidget(QuickPlotGenerator(self))
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# self.qpg_dock.setMinimumSize(self.qpg_dock.minimumSizeHint())
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# self.area.addDock(self.qpg_dock)
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self.danalyse_panel = Dock("Analyse and Fitting")
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self.analyse_panel = WidgetAnalysePanel()
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self.danalyse_panel.addWidget(self.analyse_panel)
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self.area.addDock(self.danalyse_panel, 'bottom')
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self.show()
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self.plots = {}
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@ -47,7 +54,7 @@ class MainPlotPanel(QtGui.QMainWindow):
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self.df = lyse.data()
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def add_plot_dock(self, plot_name, plot_widget, **kwargs):
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def add_plot_dock(self, plot_name, plot_widget, overlap=True, **kwargs):
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if plot_name not in self.plots:
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plot_widget.plot_name = plot_name
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@ -55,7 +62,9 @@ class MainPlotPanel(QtGui.QMainWindow):
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dock.sigClosed.connect(self.remove_plot)
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dock.addWidget(plot_widget)
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if len(self.plots):
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if overlap and len(self.plots):
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self.area.addDock(dock, 'above', relativeTo=self.area.docks[list(self.plots.keys())[-1]])
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elif len(self.plots):
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if len(self.plots) % self.n_rows == 2:
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position = 'right'
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self.area.addDock(dock, position)
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86
HelperClasses/Plotting/WidgetAnalysePanel.py
Normal file
86
HelperClasses/Plotting/WidgetAnalysePanel.py
Normal file
@ -0,0 +1,86 @@
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import pyqtgraph as pg
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from pyqtgraph import Qt
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from pyqtgraph.Qt import QtCore, QtGui
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from PyQt5.QtWidgets import *
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from PyQt5.QtCore import *
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from .DataExtractorLyse import DataExtractorManager
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class WidgetAnalysePanel(QSplitter):
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def __init__(self, **kwargs):
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super().__init__(**kwargs)
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self.setOrientation(Qt.Vertical)
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# Add title
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self.title = QtGui.QLabel()
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self.title.setAlignment(QtCore.Qt.AlignCenter)
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self.title.setText('<h2>' + 'Analyse and Fitting' + ' <\h2>')
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self.title.setFixedHeight(30)
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self.addWidget(self.title)
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self.bottom = QSplitter()
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self.addWidget(self.bottom)
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self.absorption_image = None
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self.absorption_image_plot = None
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self.absorption_image_atom_number = None
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def update_absorption_imaging_atom_number(self):
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x, y = self.absorption_image_plot.roi.pos()
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x_span, y_span = self.absorption_image_plot.roi.size()
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x = int(x)
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y = int(y)
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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
|
||||
|
||||
|
||||
@ -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()
|
||||
|
||||
|
||||
@ -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))
|
||||
self.aximg.setTitle("pos: (%0.1f, %0.1f) value: %g" % (x, y, val))
|
||||
|
||||
@ -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
|
||||
|
||||
15
test.py
15
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()
|
||||
|
||||
@ -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()
|
||||
|
||||
|
||||
@ -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)
|
||||
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user