def gui_docks_p2_04_02(d_area, _, title=None):
d1 = Dock(title, size=(1, 1), closable=True)
tab_1 = pg.TableWidget()
d1.addWidget(tab_1)
d_area.addDock(d1, 'right')
c = np.arange(2.0, 0.0, -0.1)
def solve_for_r(conc, start_r):
return root(
lambda r: -r + 1.5 * (conc - 0.8 * r) /
(1 + 0.3 * np.sqrt(conc - 0.8 * r) + 0.1 * (conc - 0.8 * r))**2.0,
np.array([start_r])).x
r_calc = np.array([solve_for_r(conc, 0.1) for conc in c]).flatten()
simple_t = -np.gradient(c) * 1 / r_calc
simple_t[0] = 0
simple_t = np.cumsum(simple_t)
quad_t = np.array([
quad(lambda conc: 1 / solve_for_r(conc, 0.1), c_min, 2.0)
for c_min in c
])[:, 0]
data = np.array([c, 1 / r_calc, simple_t, quad_t]).T
tab_1.setData(data)
tab_1.setHorizontalHeaderLabels(['c', '1/r', 't_simple', 't_quadfunc'])
tab_1.sortByColumn(2, QtCore.Qt.AscendingOrder)
tab_1.horizontalHeader().setResizeMode(QtGui.QHeaderView.ResizeToContents)
def __init__(self, title, mode="PLOT", size=None, closable=False):
if mode not in modes:
raise Exception("INvalid Mode Specified. PSecify PLOT or TABLE")
self.mode = mode
Dock.__init__(self, title, size=size, closable=closable)
self.newdata = []
self.data = []
self.refdata = []
self.startindex = 0
self.endindex = 0
self.legenditem = None
self.updateinfo = True
self.control = controlDock(title)
self.control.paused.connect(self.pausePlot)
self.control.showLegend.connect(self.showLegend)
if mode == "PLOT":
self.wid = pg.PlotWidget(title="")
self.addWidget(self.wid)
self.plotList = []
elif mode == "TABLE":
self.wid = pg.TableWidget()
self.addWidget(self.wid)
self.wid.setColumnCount(len(tableoptkeys))
self.wid.horizontalHeader().setResizeMode(QtGui.QHeaderView.Stretch)
self.tabList = []
def __init__(self, mol, parent, **kwargs):
super(TableWindow, self).__init__(parent)
kind = kwargs.get('kind', None)
if kind == 'distance':
self.setWindowTitle('Molviewer :: Distance matrix :: {:s}'.format(
mol.filename))
data = distance_matrix(mol)
table = pg.TableWidget(sortable=False)
table.setData(data)
# elif kind == 'info':
# self.setWindowTitle('MolViewer :: Info table :: {:s}'.format(mol.filename))
# data = moleculeinfo(mol)
# table = pg.TableWidget(sortable=False)
# table.setData(data)
closebutton = QtGui.QPushButton("&Close")
closebutton.setFocus()
closebutton.clicked.connect(self.close)
buttonbox = QtGui.QDialogButtonBox()
buttonbox.addButton(closebutton, QtGui.QDialogButtonBox.ActionRole)
verticalLayout = QtGui.QVBoxLayout(self)
verticalLayout.addWidget(table)
verticalLayout.addWidget(buttonbox)
def __init__(self,
topics=None,
terms=None,
addr=None,
parent=None,
**kwargs):
super().__init__(parent)
self.terms = terms
self.update_rate = kwargs.get('update_rate', 30)
self.grid = QtGui.QGridLayout(self)
self.table = pg.TableWidget()
self.last_updated = QtWidgets.QLabel(parent=self)
self.grid.addWidget(self.table, 0, 0)
self.grid.setRowStretch(0, 10)
self.grid.addWidget(self.last_updated, 1, 0)
self.fetcher = None
if addr:
self.fetcher = AsyncFetcher(topics,
terms,
addr,
parent=self,
ratelimit=1.0 / self.update_rate)
self.fetcher.start()
def set_up(self):
layout = QtGui.QHBoxLayout()
self.setLayout(layout)
# Graph
self.graph_widget = self.create_graph_widget()
self.color_map = pg.ColorMap([0, 0.5, 1], [(1., 1., 1.), (1., 1., 0.),
(1., 0.5, 0.)])
# Enriched GO terms
go_table = pg.TableWidget()
go_table.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)
go_table.clicked.connect(self.select_term)
data = np.array([(term[0], float(term[1]), len(term[2]))
for term in self.analysis.go_terms.values()],
dtype=[('GO ID', object), ('P-waarde', float),
('Eiwitten', int)])
go_table.setData(data)
# Proteins in selected GO term
proteins_container = QtGui.QWidget()
proteins_container.setLayout(QtGui.QVBoxLayout())
self.proteins_table = pg.TableWidget()
self.proteins_table.setSelectionBehavior(
QtGui.QAbstractItemView.SelectRows)
self.proteins_table.setSizePolicy(
QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding,
QtGui.QSizePolicy.Expanding))
self.graph_title = QtGui.QLabel('')
self.graph_title.setAlignment(QtCore.Qt.AlignHCenter)
self.graph_title.setOpenExternalLinks(True)
font = QtGui.QFont()
font.setBold(True)
self.graph_title.setFont(font)
self.graph_title.setWordWrap(True)
self.show_graph_button = QtGui.QPushButton('Graph')
self.show_graph_button.clicked.connect(self.show_graph)
proteins_container.layout().addWidget(self.graph_title)
proteins_container.layout().addWidget(self.proteins_table)
proteins_container.layout().addWidget(self.show_graph_button)
# Splitter with widgets
splitter = QtGui.QSplitter(self)
splitter.addWidget(go_table)
splitter.addWidget(proteins_container)
splitter.setSizes([1, 1, 1])
layout.addWidget(splitter)
def __init__(self):
QtGui.QWidget.__init__(self)
self.win = pg.TableWidget(editable=True, sortable=False)
self.layout = QtGui.QVBoxLayout()
self.layout.addWidget(self.win)
self.setLayout(self.layout)
self.win.setData([])
data.updateState.connect(self.replot)
self.win.setFormat("%.3f")
def showMetadata(self):
"""
Show Metadata information in the table
"""
self.w = pg.TableWidget()
self.w.show()
self.w.resize(500, 900)
self.w.setData(self.file['Metadata/Metadata'][:])
def setupUi(self):
"""Set up the UI for tomography plugin"""
self.toolbar = Toolbar()
self.centerwidget = QtGui.QTabWidget()
self.centerwidget.setDocumentMode(True)
self.centerwidget.setTabsClosable(True)
self.bottomwidget = viewers.RunConsole()
self.functionwidget = QUiLoader().load('xicam/gui/tomographyleft.ui')
self.functionwidget.functionsList.setAlignment(QtCore.Qt.AlignBottom)
self.functionwidget.addFunctionButton.setToolTip('Add function to pipeline')
self.functionwidget.clearButton.setToolTip('Clear pipeline')
self.functionwidget.fileButton.setToolTip('Save/Load pipeline')
self.functionwidget.moveDownButton.setToolTip('Move selected function down')
self.functionwidget.moveUpButton.setToolTip('Move selected function up')
self.addfunctionmenu = QtGui.QMenu()
self.functionwidget.addFunctionButton.setMenu(self.addfunctionmenu)
self.functionwidget.addFunctionButton.setPopupMode(QtGui.QToolButton.ToolButtonPopupMode.InstantPopup)
self.functionwidget.addFunctionButton.setArrowType(QtCore.Qt.NoArrow)
filefuncmenu = QtGui.QMenu()
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap("xicam/gui/icons_55.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.openaction = QtGui.QAction(icon, 'Open', filefuncmenu)
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap("xicam/gui/icons_59.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.saveaction = QtGui.QAction(icon, 'Save', filefuncmenu)
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap("xicam/gui/icons_56.png"), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.refreshaction = QtGui.QAction(icon, 'Reset', filefuncmenu)
filefuncmenu.addActions([self.openaction, self.saveaction, self.refreshaction])
self.functionwidget.fileButton.setMenu(filefuncmenu)
self.functionwidget.fileButton.setPopupMode(QtGui.QToolButton.ToolButtonPopupMode.InstantPopup)
self.functionwidget.fileButton.setArrowType(QtCore.Qt.NoArrow)
leftwidget = QtGui.QSplitter(QtCore.Qt.Vertical)
paramtree = pt.ParameterTree()
self.param_form = QtGui.QStackedWidget()
self.param_form.addWidget(paramtree)
self.property_table = pg.TableWidget()
self.property_table.verticalHeader().hide()
self.property_table.horizontalHeader().setStretchLastSection(True)
self.property_table.setSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Expanding)
leftwidget.addWidget(self.param_form)
leftwidget.addWidget(self.functionwidget)
icon_functions = QtGui.QIcon(QtGui.QPixmap("xicam/gui/icons_49.png"))
icon_properties = QtGui.QIcon(QtGui.QPixmap("xicam/gui/icons_61.png")) #metadata icon
self.leftmodes = [(leftwidget, icon_functions),(self.property_table,icon_properties)]
def __init__(self):
QtGui.QStackedWidget.__init__(self)
self.widgets = {}
self.widgets['empty'] = QtGui.QWidget()
self.widgets['table'] = pg.TableWidget()
self.widgets['text'] = QtGui.QTextBrowser()
self.widgets['plot'] = pg.PlotWidget()
self.widgets['image'] = pg.ImageView()
for w in self.widgets.values():
self.addWidget(w)
self.clear()
def __init__(self,parent=None,pvType='Motor'):
QWidget.__init__(self,parent)
self.pvType=pvType
self.layout=pg.LayoutWidget()
self.addPVButton=QPushButton('Add '+self.pvType)
self.addPVButton.clicked.connect(self.addPV)
self.removePVButton=QPushButton('Remove '+self.pvType)
self.removePVButton.clicked.connect(self.removePVs)
self.layout.addWidget(self.addMotorButton,row=0,col=0)
self.layout.addWidget(self.removeMotorButton,row=0,col=1)
self.PVTable=pg.TableWidget(editable=True,sortable=True)
self.layout.addWidget(self.PVTable,row=1,col=0,colspan=2)
def __init__(self, data):
col_selection_TemplateBaseClass.__init__(self)
# Create the param window
self.ui = col_selection_WindowTemplate()
self.ui.setupUi(self)
self.ui.done_pushButton.clicked.connect(self.done)
self.table_widget = pg.TableWidget()
self.ui.data_preview_groupBox.layout().addWidget(self.table_widget)
self.table_widget.setData(data)
#self.setWindowFlag(QtCore.Qt.WindowCloseButtonHint, False)
self.show()
def __init__(self, parent=None):
super(DetailFirstrowdata, self).__init__(parent)
# self.resize(400,500)
# 设置好的布局 已经保证可以完全填充窗体
self.mylayout = QGridLayout(self)
self.mylayout.setObjectName("gridLayout")
self.firstrow = pg.TableWidget() # 下面是手动添加信息，需要改变
self.firstrowdata = [(1156, '0.001001', '192.168.0.101',
'221.15.13.15', 'Tcp', '62', 'syn = 2123'),
(1157, '0.101001', '192.168.0.101',
'221.15.13.15', 'Tcp', '62', 'syn = 2235'),
(1158, '1.001001', '92.168.0.101', '221.15.13.15',
'Tcp', '15', 'syn = 2152'),
(1159, '10.001001', '192.168.0.101',
'121.15.13.15', 'Tcp', '25', 'syn = 2365'),
(1160, '2.001001', '192.168.0.101', '58.15.13.15',
'Tcp', '85', 'syn = 2155')]
# np 可以不用，这个更方便的定义了数据格式
self.showfirstrowdata = np.array(self.firstrowdata,
dtype=[('No', int), ('Time', object),
('Source', object),
('Destination', object),
('Protocol', object),
('Length', object),
('Info', object)])
self.firstrow.setData(self.showfirstrowdata)
self.mylayout.addWidget(self.firstrow)
self.firstrow.setShowGrid(False) # 是否显示网格线
self.firstrow.verticalHeader().setHidden(True) # 垂直方向的表头删除
# self.bottomwindow.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch()) TypeError: 'ResizeMode' object is not callable
self.firstrow.setColumnWidth(0, 130) # 设置列宽
self.firstrow.setColumnWidth(1, 180)
self.firstrow.setColumnWidth(2, 300)
self.firstrow.setColumnWidth(3, 300)
self.firstrow.setColumnWidth(4, 130)
self.firstrow.setColumnWidth(5, 130)
self.firstrow.horizontalHeader().setStretchLastSection(
True) # 最后一个随机全部占满剩余空间
self.firstrow.setSelectionBehavior(
QAbstractItemView.SelectRows) # 选中一个 选中整行
self.firstrow.setFrameShape(QFrame.NoFrame)
# self.bottomwindow.horizontalHeader().setSectionResizeMode(1,QHeaderView.Stretch())
# self.bottomwindow.horizontalHeader().setResizeMode(1,QHeaderView.ResizeToContents()Stretch)
self.setLayout(self.mylayout)
self.timer1 = threading.Timer(
0.4, self.putnumofdecode) # 这个是为了显示那个，第一栏显示数据的速度的
self.timer1.start()
def __init__(self, title, **kwargs):
super().__init__(**kwargs)
self.table = pg.TableWidget()
self.bottom.addWidget(self.table)
self.desciption = pg.LayoutWidget()
self.title = QtGui.QLabel()
self.title.setAlignment(QtCore.Qt.AlignCenter)
self.title.setText('<h2>' + title + ' <\h2>')
self.warning = QtGui.QLabel()
self.warning.setAlignment(QtCore.Qt.AlignCenter)
self.desciption.addWidget(self.title)
self.desciption.nextRow()
self.desciption.addWidget(self.warning)
self.bottom.addWidget(self.desciption)
def __init__(self, path, sequence_length):
QWidget.__init__(self)
bowtie_result_file = path
found_primer_data, header, query_name = self.create_data(bowtie_result_file)
# Set title and size
self.setWindowTitle('Primers found for query ' + query_name)
self.resize(1000, 793)
# Table
table_window = pg.TableWidget()
table_window.setData(found_primer_data)
table_window.setHorizontalHeaderLabels(header)
table_window.setColumnWidth(0, 200)
table_window.setColumnWidth(1, 150)
table_window.setColumnWidth(2, 150)
table_window.setColumnWidth(3, 250)
table_window.setColumnWidth(4, 150)
graphic_window = GraphDisplay(found_primer_data, query_name, sequence_length)
layout = QVBoxLayout(self)
layout.addWidget(table_window)
layout.addWidget(graphic_window)
self.setLayout(layout)
def __init__(self, parent=None):
self.sweeps = []
self.channels = []
self.current_event_set = None
self.event_sets = []
QtGui.QWidget.__init__(self, parent)
self.layout = QtGui.QGridLayout()
self.setLayout(self.layout)
self.layout.setContentsMargins(0, 0, 0, 0)
self.vsplit = QtGui.QSplitter(QtCore.Qt.Vertical)
self.layout.addWidget(self.vsplit, 0, 0)
self.pre_plot = pg.PlotWidget()
self.post_plot = pg.PlotWidget()
for plt in (self.pre_plot, self.post_plot):
plt.setClipToView(True)
plt.setDownsampling(True, True, 'peak')
self.post_plot.setXLink(self.pre_plot)
self.vsplit.addWidget(self.pre_plot)
self.vsplit.addWidget(self.post_plot)
self.response_plots = PlotGrid()
self.vsplit.addWidget(self.response_plots)
self.event_splitter = QtGui.QSplitter(QtCore.Qt.Horizontal)
self.vsplit.addWidget(self.event_splitter)
self.event_table = pg.TableWidget()
self.event_splitter.addWidget(self.event_table)
self.event_widget = QtGui.QWidget()
self.event_widget_layout = QtGui.QGridLayout()
self.event_widget.setLayout(self.event_widget_layout)
self.event_splitter.addWidget(self.event_widget)
self.event_splitter.setSizes([600, 100])
self.event_set_list = QtGui.QListWidget()
self.event_widget_layout.addWidget(self.event_set_list, 0, 0, 1, 2)
self.event_set_list.addItem("current")
self.event_set_list.itemSelectionChanged.connect(
self.event_set_selected)
self.add_set_btn = QtGui.QPushButton('add')
self.event_widget_layout.addWidget(self.add_set_btn, 1, 0, 1, 1)
self.add_set_btn.clicked.connect(self.add_set_clicked)
self.remove_set_btn = QtGui.QPushButton('del')
self.event_widget_layout.addWidget(self.remove_set_btn, 1, 1, 1, 1)
self.remove_set_btn.clicked.connect(self.remove_set_clicked)
self.fit_btn = QtGui.QPushButton('fit all')
self.event_widget_layout.addWidget(self.fit_btn, 2, 0, 1, 2)
self.fit_btn.clicked.connect(self.fit_clicked)
self.fit_plot = PlotGrid()
self.fit_explorer = None
self.artifact_remover = ArtifactRemover(user_width=True)
self.baseline_remover = BaselineRemover()
self.filter = SignalFilter()
self.params = pg.parametertree.Parameter(
name='params',
type='group',
children=[{
'name': 'pre',
'type': 'list',
'values': []
}, {
'name': 'post',
'type': 'list',
'values': []
}, self.artifact_remover.params, self.baseline_remover.params,
self.filter.params, {
'name': 'time constant',
'type': 'float',
'suffix': 's',
'siPrefix': True,
'value': 10e-3,
'dec': True,
'minStep': 100e-6
}])
self.params.sigTreeStateChanged.connect(self._update_plots)
def spikesort_gui(load_previous_dataset=True):
def load_config():
global raw_data
global sampling_frequency
global number_of_channels_in_binary_file
global prb_file
global duration_of_time_plot
global spike_info
global channel_map
global num_of_shanks_for_vis
config = configparser.ConfigParser()
config.read(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
'defaults.ini'))
if not 'SPIKES' in config:
return
all_exist = True
spike_info_file = config['SPIKES']['spike_info_file']
if 'spike_info.df' in spike_info_file:
spike_info = pd.read_pickle(spike_info_file)
update_templates_table()
generate_scater_plot()
file_name = config['BINARY DATA FILE']['binary_data_filename']
if not os.path.isfile(file_name):
all_exist = False
prb_file = config['PROBE']['prb_file']
if not os.path.isfile(prb_file):
all_exist = False
channel_map_file = config['PROBE']['channel_map_file']
if not os.path.isfile(channel_map_file):
all_exist = False
else:
channel_map = np.squeeze(np.load(channel_map_file))
if all_exist:
type = config['BINARY DATA FILE']['type']
types = {
'int16': np.int16,
'uint16': np.uint16,
'int32': np.int32,
'uint32': np.uint32,
'int64': np.int64,
'uint32': np.uint64,
'float16': np.float16,
'float32': np.float32,
'float64': np.float64
}
number_of_channels_in_binary_file = int(
config['BINARY DATA FILE']
['number_of_channels_in_binary_file'])
order = config['BINARY DATA FILE']['order']
raw_data = np.memmap(file_name, mode='r', dtype=types[type])
raw_data = np.reshape(raw_data,
(number_of_channels_in_binary_file,
int(raw_data.shape[0] /
number_of_channels_in_binary_file)),
order=order)
sampling_frequency = int(
config['BINARY DATA FILE']['sampling_frequency'])
electrodes = len(channel_map)
for i in range(electrodes):
electrode_curve = pg.PlotCurveItem()
spikes_time_plot.addItem(electrode_curve)
avg_electrode_curves.append(electrode_curve)
duration_of_time_plot = float(
config['TIME PLOT']['duration_of_time_plot'])
num_of_shanks_for_vis = config['PROBE'][
'num_of_shanks_for_vis']
if num_of_shanks_for_vis != 'None':
num_of_shanks_for_vis = int(num_of_shanks_for_vis)
else:
num_of_shanks_for_vis = None
else:
print(
'Some file paths in the configuration file do not point to existing files. '
'Load your data manually')
elif spike_info_file == 'empty':
print('Configuration file is empty. Load your data manually')
def action_load_new_data():
config = configparser.ConfigParser()
config.read(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
'defaults.ini'))
if config['SPIKES']['spike_info_file'] == 'empty':
directory = None
else:
directory = os.path.dirname(config['SPIKES']['spike_info_file'])
fname = QtWidgets.QFileDialog.getOpenFileName(
caption='Load spike_info.df file', directory=directory)
spike_info_file = fname[0]
if 'spike_info.df' in spike_info_file:
config['SPIKES']['spike_info_file'] = spike_info_file
else:
print('Point to a file named spike_info.df')
return
fname = QtWidgets.QFileDialog.getOpenFileName(
caption='Load binary data file', directory=directory)
binary_data_filename = fname[0]
config['BINARY DATA FILE'][
'binary_data_filename'] = binary_data_filename
fname = QtWidgets.QFileDialog.getOpenFileName(caption='Load prb file',
directory=directory)
prb_file = fname[0]
config['PROBE']['prb_file'] = prb_file
fname = QtWidgets.QFileDialog.getOpenFileName(
caption='Load channel map file', directory=directory)
channel_map_file = fname[0]
config['PROBE']['channel_map_file'] = channel_map_file
types = {
'int16': np.int16,
'uint16': np.uint16,
'int32': np.int32,
'uint32': np.uint32,
'int64': np.int64,
'uint64': np.uint64,
'float16': np.float16,
'float32': np.float32,
'float64': np.float64
}
type, ok = QtWidgets.QInputDialog.getItem(
central_window,
'Binary Data Type', 'Input the type of the binary data file',
sorted(list(types.keys())))
if ok:
config['BINARY DATA FILE']['type'] = type
order, ok = QtWidgets.QInputDialog.getItem(
central_window, 'Binary Data Order',
'Input the order of the binary data file', ['F', 'C'])
if ok:
config['BINARY DATA FILE']['order'] = order
sampling_frequency, ok = QtWidgets.QInputDialog.getInt(
central_window, 'Sampling Frequency',
'Input the sampling frequency of the binary data', 30000, 1000,
100000, 1)
if ok:
config['BINARY DATA FILE']['sampling_frequency'] = str(
sampling_frequency)
number_of_channels_in_binary_file, ok = QtWidgets.QInputDialog.getInt(
central_window, 'Number of Channels in Binary File',
'Input the total number of channels in '
'the binary data', 128, 4, 10000, 1)
if ok:
config['BINARY DATA FILE'][
'number_of_channels_in_binary_file'] = str(
number_of_channels_in_binary_file)
duration_of_time_plot, ok = QtWidgets.QInputDialog.getInt(
central_window, 'Duration of Time Plot',
'Input the duration of the time plot in ms', 4, 1, 20, 1)
if ok:
config['TIME PLOT']['duration_of_time_plot'] = str(
duration_of_time_plot / 1000)
num_of_shanks_for_vis, ok = QtWidgets.QInputDialog.getItem(
central_window, 'Number of Shanks for Visual',
'Input the number of pieces the probe should be '
'visualized in (for long single shank probes). '
'Use None for multi-shank probes with shanks '
'defined in the prb file', ['None', '1', '2', '3', '4', '5', '6'])
if ok:
config['PROBE']['num_of_shanks_for_vis'] = num_of_shanks_for_vis
with open(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
'defaults.ini'), 'w') as configfile:
config.write(configfile)
load_config()
def action_save_info():
global spike_info
fname = QtWidgets.QFileDialog.getExistingDirectory(
caption='Select directory to save the new '
'spike_info.pd file. Any existing'
' spike_info.pd file will be overwritten.')
print(fname)
spike_info.to_pickle(os.path.join(fname, 'spike_info.df'))
config = configparser.ConfigParser()
config.read('defaults.ini')
config.set('SPIKES', 'spike_info_file',
os.path.join(fname, 'spike_info.df'))
with open('defaults.ini', 'w') as configfile:
config.write(configfile)
def action_undo_template_assignment():
global currently_selected_spikes
global currently_selected_templates
spike_info.loc[currently_selected_spikes,
'template_after_sorting'] = spike_info.loc[
currently_selected_spikes,
'template_after_cleaning']
spike_info.loc[currently_selected_spikes,
'type_after_sorting'] = spike_info.loc[
currently_selected_spikes, 'type_after_cleaning']
update_templates_table()
def on_roi_selection(all_rois, freeform=False):
global currently_selected_spikes
global currently_selected_templates
global selectable_spikes
global on_spikes
global tsne_spots
global spike_info
currently_selected_spikes = np.empty(0)
points = np.array(
[tsne_spots[i]['pos'] for i in range(len(tsne_spots))])
for i in range(len(all_rois)):
if not freeform:
shape = all_rois[i].parentBounds()
bounds = shape
else:
shape = all_rois[i].shape()
bounds = shape.boundingRect()
selected = np.argwhere(
(points[:, 0] > bounds.x()) *
(points[:, 0] < bounds.x() + bounds.width()) *
(points[:, 1] > bounds.y()) *
(points[:, 1] < bounds.y() + bounds.height())).flatten()
if freeform:
currently_selected_spikes = np.append(
currently_selected_spikes, [
i for i in selected if shape.contains(
QtCore.QPointF(points[i][0], points[i][1]))
])
else:
currently_selected_spikes = np.append(
currently_selected_spikes, selected)
all_selectable_spikes = np.intersect1d(selectable_spikes, on_spikes)
currently_selected_spikes = currently_selected_spikes[np.in1d(
currently_selected_spikes, all_selectable_spikes)]
currently_selected_templates = hf.find_templates_of_spikes(
spike_info, currently_selected_spikes)
selected_templates_text_box.setText('Selected templates: ' + ', '.join(
str(template) for template in currently_selected_templates))
print('Number of spikes selected: ' +
str(len(currently_selected_spikes)))
show_selected_points()
def on_roi_deletion():
global currently_selected_spikes
global currently_selected_templates
currently_selected_spikes = np.empty(0)
currently_selected_templates = np.empty(0)
def show_selected_points():
global spike_info
scatter_selected_item.clear()
scatter_selected_item.setData(pos=np.array([
spike_info['tsne_x'].iloc[currently_selected_spikes].values,
spike_info['tsne_y'].iloc[currently_selected_spikes].values
]).T)
scatter_selected_item.setBrush((255, 255, 255))
def generate_scater_plot():
global number_of_spikes
global selectable_spikes
global on_spikes
global tsne_spots
global spike_info
global all_points_brush
global all_points_symbols
scatter_item.clear()
scatter_selected_item.clear()
number_of_spikes = len(spike_info)
selectable_spikes = np.arange(number_of_spikes)
on_spikes = selectable_spikes
number_of_templates = len(
np.unique(spike_info['template_after_sorting']))
progdialog = QtWidgets.QProgressDialog()
progdialog.setGeometry(500, 500, 400, 40)
progdialog.setWindowTitle('Loading t-sne plot')
progdialog.setMinimum(0)
progdialog.setMaximum(5)
progdialog.setWindowModality(QtCore.Qt.WindowModal)
progdialog.setLabelText(
'Generating colors _____________________________________')
progdialog.show()
progdialog.setValue(0)
QtWidgets.QApplication.processEvents()
color = [
pg.intColor(spike_info['template_after_sorting'].iloc[i],
hues=number_of_templates,
values=1,
maxValue=255,
minValue=150,
maxHue=360,
minHue=0,
sat=255,
alpha=255) for i in range(number_of_spikes)
]
progdialog.setLabelText(
'Generating brushes ____________________________________')
progdialog.setValue(1)
brush = [pg.mkBrush(color[i]) for i in range(number_of_spikes)]
all_points_brush = brush
progdialog.setLabelText(
'Generating positions __________________________________')
progdialog.setValue(2)
tsne_spots = [{
'pos':
[spike_info['tsne_x'].iloc[i], spike_info['tsne_y'].iloc[i]],
'data':
1,
'brush':
brush[i],
'size':
2
} for i in range(number_of_spikes)]
progdialog.setLabelText(
'Adding points to plot __________________________________')
progdialog.setValue(3)
scatter_item.addPoints(tsne_spots)
progdialog.setLabelText(
'Generating symbols ... Almost done ______________________')
progdialog.setValue(4)
symbol = []
for i in range(number_of_spikes):
symbol.append(
hf.symbol_from_type(spike_info['type_after_sorting'].iloc[i]))
scatter_item.setSymbol(symbol)
all_points_symbols = symbol
progdialog.setValue(5)
progdialog.close()
def update_average_spikes_plot():
global currently_selected_spikes
global data_of_selected_spikes
global spike_info
global channel_map
electrodes = len(channel_map)
half_duration = duration_of_time_plot / 2
time_points = int(half_duration * sampling_frequency)
time_axis = np.arange(-half_duration, half_duration,
1 / sampling_frequency)
data_of_selected_spikes = np.zeros((electrodes, 2 * time_points))
times = spike_info['times'].iloc[currently_selected_spikes]
progdialog = QtWidgets.QProgressDialog()
progdialog.setMinimum(0)
progdialog.setMaximum(len(times))
progdialog.setWindowTitle('Loading spikes')
progdialog.setGeometry(500, 500, 400, 40)
progdialog.setWindowModality(QtCore.Qt.WindowModal)
progdialog.show()
prog = 0
for t in times:
add_data = raw_data[channel_map,
int(t - time_points):int(t + time_points)]
data_of_selected_spikes = data_of_selected_spikes + add_data
prog += 1
if prog % 100 == 0:
progdialog.setValue(prog)
progdialog.setLabelText('Loading spike: ' + str(prog) +
' of ' + str(len(times)))
QtWidgets.QApplication.processEvents()
data_of_selected_spikes = data_of_selected_spikes / len(times)
for i in np.arange(electrodes):
avg_electrode_curves[i].setData(time_axis,
data_of_selected_spikes[i, :])
avg_electrode_curves[i].setPen(
pg.mkPen(color=(i, number_of_channels_in_binary_file * 1.3),
width=0.5))
progdialog.setValue(len(times))
progdialog.close()
def update_templates_table():
global number_of_spikes
global spike_info
templates_table.setData(
hf.get_templates_with_number_of_spikes_from_spike_info(spike_info))
templates_table.setHorizontalHeaderLabels(
['Template number', 'Number of spikes in template'])
templates_table.setSelectionMode(
QtGui.QAbstractItemView.ExtendedSelection)
templates_table.setSelectionBehavior(
QtGui.QAbstractItemView.SelectRows)
header = templates_table.horizontalHeader()
header.setResizeMode(0, QtGui.QHeaderView.ResizeToContents)
header.setResizeMode(1, QtGui.QHeaderView.ResizeToContents)
def update_heatmap_plot():
global data_of_selected_spikes
global channel_map
global number_of_channels_in_binary_file
global num_of_shanks_for_vis
connected = channel_map
connected_binary = np.in1d(
np.arange(number_of_channels_in_binary_file), connected)
bad_channels = np.squeeze(
np.argwhere(connected_binary == False).astype(np.int))
sh.create_heatmap_on_matplotlib_widget(
heatmap_plot,
data_of_selected_spikes,
prb_file,
window_size=60,
bad_channels=bad_channels,
num_of_shanks=num_of_shanks_for_vis,
rotate_90=True,
flip_ud=False,
flip_lr=False)
heatmap_plot.draw()
def update_autocorelogram():
global currently_selected_spikes
global spike_info
spike_times = spike_info['times'].iloc[
currently_selected_spikes].values.astype(np.int64)
diffs, norm = hf.crosscorrelate_spike_trains(spike_times,
spike_times,
lag=1000)
hist, edges = np.histogram(diffs, bins=50)
autocorelogram_curve.setData(x=edges,
y=hist,
stepMode=True,
fillLevel=0,
brush=(0, 0, 255, 150))
# On press button functions ---------
def on_press_button_update():
update_average_spikes_plot()
update_autocorelogram()
update_heatmap_plot()
def on_tsne_filter_for_type_combo_box_change(index):
global number_of_spikes
global spike_info
global on_spikes
global all_points_brush
state = tsne_color_scheme_combo_box.currentIndex()
if state == 0:
type_state = 'type_after_sorting'
template_state = 'template_after_sorting'
else:
type_state = 'type_after_cleaning'
template_state = 'template_after_cleaning'
if index > 0:
type_to_show = hf.template_types[index]
spikes_to_show = np.array(spike_info[spike_info[type_state] ==
type_to_show].index.values)
elif index == 0:
spikes_to_show = range(number_of_spikes)
on_spikes = spikes_to_show
progdialog = QtWidgets.QProgressDialog()
progdialog.setGeometry(500, 500, 400, 40)
progdialog.setWindowTitle('Filtering t-SNE according to type')
progdialog.setMinimum(0)
progdialog.setWindowModality(QtCore.Qt.WindowModal)
progdialog.setLabelText(
'Generating colors and symbols ... ')
progdialog.show()
progdialog.setValue(0)
QtWidgets.QApplication.processEvents()
color_scheme = spike_info[template_state]
brush = list(all_points_brush)
spikes_to_hide = np.array(
range(number_of_spikes)
)[~np.in1d(np.array(range(number_of_spikes)), spikes_to_show)]
i = 0
progdialog.setMaximum(len(spikes_to_hide))
for s in spikes_to_hide:
brush[s] = pg.intColor(color_scheme.iloc[s],
hues=50,
values=1,
maxValue=255,
minValue=150,
maxHue=360,
minHue=0,
sat=255,
alpha=0)
if i % 10000 == 0:
progdialog.setValue(i)
progdialog.setLabelText('Hiding spikes ' + str(i) + ' of ' +
str(len(spikes_to_hide)) + ' spikes.')
QtWidgets.QApplication.processEvents()
i = i + 1
progdialog.setMaximum(2)
progdialog.setLabelText(
'Applying colors ... ')
progdialog.setValue(1)
QtWidgets.QApplication.processEvents()
scatter_item.setBrush(brush)
progdialog.setValue(2)
progdialog.close()
def on_tsne_color_scheme_combo_box_change(index):
global number_of_spikes
global spike_info
global all_points_brush
progdialog = QtWidgets.QProgressDialog()
progdialog.setGeometry(500, 500, 400, 40)
progdialog.setWindowTitle('Changing spike color scheme')
progdialog.setMinimum(0)
progdialog.setMaximum(2)
progdialog.setWindowModality(QtCore.Qt.WindowModal)
progdialog.setLabelText(
'Generating colors and symbols ... ')
progdialog.show()
progdialog.setValue(0)
QtWidgets.QApplication.processEvents()
spikes_to_change = range(number_of_spikes)
print(index)
if index == 0:
number_of_templates = len(
np.unique(spike_info['template_after_sorting']))
color_scheme = spike_info['template_after_sorting']
brush = [
pg.intColor(color_scheme.iloc[i],
hues=number_of_templates,
values=1,
maxValue=255,
minValue=150,
maxHue=360,
minHue=0,
sat=255,
alpha=255) for i in spikes_to_change
]
symbol = []
for i in spikes_to_change:
symbol.append(
hf.symbol_from_type(
spike_info['type_after_sorting'].iloc[i]))
elif index == 1:
number_of_templates = len(
np.unique(spike_info['template_after_cleaning']))
color_scheme = spike_info['template_after_cleaning']
brush = [
pg.intColor(color_scheme.iloc[i],
hues=number_of_templates,
values=1,
maxValue=255,
minValue=150,
maxHue=360,
minHue=0,
sat=255,
alpha=255) for i in spikes_to_change
]
symbol = []
for i in spikes_to_change:
symbol.append(
hf.symbol_from_type(
spike_info['type_after_cleaning'].iloc[i]))
progdialog.setValue(1)
progdialog.setLabelText(
'Applying colors and symbols ... ')
QtWidgets.QApplication.processEvents()
all_points_brush = brush
scatter_item.setBrush(brush)
scatter_item.setSymbol(symbol)
progdialog.setValue(2)
progdialog.close()
def on_press_button_freeze_spikes():
global selectable_spikes
global currently_selected_spikes
global number_of_spikes
selectable_spikes = np.array(range(number_of_spikes))[~np.in1d(
np.array(range(number_of_spikes)), currently_selected_spikes)]
def on_press_button_unfreeze_all():
global selectable_spikes
global number_of_spikes
selectable_spikes = np.array(range(number_of_spikes))
def on_templates_table_selection():
global currently_selected_templates
global currently_selected_spikes
global spike_info
currently_selected_templates = []
rows_selected = templates_table.selectedItems()
for i in np.arange(0, len(rows_selected), 2):
currently_selected_templates.append(int(rows_selected[i].text()))
currently_selected_templates = np.array(currently_selected_templates)
currently_selected_spikes = np.empty(0)
for selected_template in currently_selected_templates:
currently_selected_spikes = np.append(
currently_selected_spikes,
spike_info.loc[spike_info['template_after_sorting'] ==
selected_template].index)
show_selected_points()
def on_press_button_show_cross_correlograms():
global currently_selected_templates
global spike_info
num_of_templates = len(currently_selected_templates)
if num_of_templates > 1:
cross_cor_window.show()
num_of_windows = (num_of_templates**2 -
num_of_templates) / 2 + num_of_templates
cross_corelogram_plots = []
column = 0
row = 0
width = 1
height = 1
progdialog = QtWidgets.QProgressDialog()
progdialog.setMinimum(0)
progdialog.setMaximum(num_of_windows)
progdialog.setWindowTitle('Making cross correlograms')
progdialog.setGeometry(500, 500, 400, 40)
progdialog.setWindowModality(QtCore.Qt.WindowModal)
progdialog.show()
prog = 0
for window_index in np.arange(num_of_windows):
cross_corelogram_plots.append(pg.PlotWidget())
cross_cor_grid_layout.addWidget(cross_corelogram_plots[-1],
column, row, height, width)
spike_times_a = spike_info['times'].loc[
spike_info['template_after_sorting'] ==
currently_selected_templates[column]].values.astype(
np.int64)
spike_times_b = spike_info['times'].loc[
spike_info['template_after_sorting'] ==
currently_selected_templates[row]].values.astype(np.int64)
diffs, norm = hf.crosscorrelate_spike_trains(spike_times_a,
spike_times_b,
lag=3000)
cross_corelogram_curve = pg.PlotCurveItem()
cross_corelogram_plots[-1].addItem(cross_corelogram_curve)
hist, edges = np.histogram(diffs, bins=100)
cross_corelogram_curve.setData(x=edges,
y=hist,
stepMode=True,
fillLevel=0,
brush=(0, 0, 255, 150))
row += width
if row > column:
column += height
row = 0
prog += 1
progdialog.setValue(prog)
progdialog.setLabelText('Making cross correlogram: ' +
str(prog) + ' of ' +
str(num_of_windows))
QtWidgets.QApplication.processEvents()
progdialog.setValue(num_of_windows)
progdialog.close()
def on_press_button_remove_from_template():
global currently_selected_spikes
global spike_info
if len(currently_selected_spikes) > 0:
spike_info.loc[currently_selected_spikes,
'template_after_sorting'] = 0
update_templates_table()
def on_press_button_make_template():
global currently_selected_spikes
global spike_info
global all_points_brush
if len(currently_selected_spikes) > 0:
all_templates = spike_info['template_after_sorting'].values
max_template = np.max(all_templates)
index, ok = QtWidgets.QInputDialog.getInt(
central_window, 'New Template Index',
'Input the index of the new template', max_template + 1, 1,
max_template + 10000, 1)
if ok:
spike_info.loc[currently_selected_spikes,
'template_after_sorting'] = index
list_of_types = [
'Noise', 'Single Unit', 'Single Unit Contaminated',
'Single Unit Putative', 'MUA', 'Unspecified 1',
'Unspecified 2', 'Unspecified 3'
]
item, ok = QtWidgets.QInputDialog.getItem(
central_window, 'New Template Type',
'Input the type of the new template', list_of_types)
if ok:
spike_info.loc[currently_selected_spikes,
'type_after_sorting'] = hf.template_types[
list_of_types.index(item)]
update_templates_table()
# ----------------------------------
# Main Window ----------------------
app = QtGui.QApplication([])
main_window = QtGui.QMainWindow()
main_toolbar = main_window.addToolBar('Tools')
main_window.setWindowTitle('Spikesort on T-sne')
main_window.resize(1300, 900)
central_window = pg.GraphicsLayoutWidget()
main_window.setCentralWidget(central_window)
grid_layout = QtGui.QGridLayout()
central_window.setLayout(grid_layout)
# ----------------------------------
# T-sne Scatter Plot ---------------
custom_viewbox = cv.CustomViewBox()
scatter_plot = pg.PlotWidget(title='T-sne plot', viewBox=custom_viewbox)
grid_layout.addWidget(scatter_plot, 0, 0, 2, 4)
scatter_plot.plotItem.ctrlMenu = None
scatter_plot.scene().contextMenu = None
scatter_item = pg.ScatterPlotItem(size=7, pen=None, pxMode=True)
scatter_plot.addItem(scatter_item)
scatter_selected_item = pg.ScatterPlotItem(size=8, pen=None, pxMode=True)
scatter_plot.addItem(scatter_selected_item)
# ---------------------------------
# Average spike time course plot --
spikes_time_plot = pg.PlotWidget(
title='Average time plot of selected spikes')
grid_layout.addWidget(spikes_time_plot, 2, 0, 2, 2)
# ---------------------------------
# Autocorelogram plot -------------
autocorelogram_plot = pg.PlotWidget(title='Autocorrelogram')
grid_layout.addWidget(autocorelogram_plot, 2, 2, 2, 2)
autocorelogram_curve = pg.PlotCurveItem()
autocorelogram_plot.addItem(autocorelogram_curve)
# ---------------------------------
# Heatmap plot --------------------
heatmap_plot = matplotlib_widget.MatplotlibWidget(toolbar_on=False)
grid_layout.addWidget(heatmap_plot, 0, 4, 6, 2)
# ---------------------------------
# Templates Table widget -----------
templates_table = pg.TableWidget(editable=False, sortable=True)
templates_table.cellClicked.connect(on_templates_table_selection)
grid_layout.addWidget(templates_table, 0, 6, 3, 1)
# ----------------------------------
# Cross correlogram window ---------
cross_cor_window = QtGui.QMainWindow()
cross_cor_window.setWindowTitle('Cross correlograms')
cross_cor_window.resize(1300, 900)
central_cross_cor_window = pg.GraphicsLayoutWidget()
cross_cor_window.setCentralWidget(central_cross_cor_window)
cross_cor_grid_layout = QtGui.QGridLayout()
central_cross_cor_window.setLayout(cross_cor_grid_layout)
# ----------------------------------
# Tool bar -------------------------
current_path = os.path.dirname(os.path.realpath(__file__))
scroll_icon_file = os.path.join(current_path, 'Icons', 'scroll_icon.png')
zoom_icon_file = os.path.join(current_path, 'Icons', 'zoom_icon.png')
select_icon_file = os.path.join(current_path, 'Icons', 'select_icon.png')
select_freeform_icon_file = os.path.join(current_path, 'Icons',
'select_freeform_icon.png')
undo_icon_file = os.path.join(current_path, 'Icons', 'undo_icon.jpg')
menu_bar = main_window.menuBar()
file_menu = menu_bar.addMenu('File')
load_data = QtWidgets.QAction('Load Data', main_window)
load_data.triggered.connect(action_load_new_data)
file_menu.addAction(load_data)
save_info = QtWidgets.QAction('Save spike info', main_window)
save_info.triggered.connect(action_save_info)
file_menu.addAction(save_info)
scroll = QtWidgets.QAction(QtGui.QIcon(scroll_icon_file), "scroll",
main_window)
scroll.triggered.connect(custom_viewbox.set_to_pan_mode)
main_toolbar.addAction(scroll)
zoom = QtWidgets.QAction(QtGui.QIcon(zoom_icon_file), "zoom", main_window)
zoom.triggered.connect(custom_viewbox.set_to_rect_mode)
main_toolbar.addAction(zoom)
select = QtWidgets.QAction(QtGui.QIcon(select_icon_file), "select",
main_window)
select.triggered.connect(custom_viewbox.draw_square_roi)
main_toolbar.addAction(select)
select_freeform = QtWidgets.QAction(QtGui.QIcon(select_freeform_icon_file),
'select freeform', main_window)
select_freeform.triggered.connect(custom_viewbox.draw_freeform_roi)
custom_viewbox.connect_on_roi_select = on_roi_selection
custom_viewbox.connect_on_roi_delete = on_roi_deletion
main_toolbar.addAction(select_freeform)
undo_assignment = QtWidgets.QAction(
QtGui.QIcon(undo_icon_file),
'assign selected spikes back to their original templates', main_window)
undo_assignment.triggered.connect(action_undo_template_assignment)
main_toolbar.addAction(undo_assignment)
# ----------------------------------
# Buttons --------------------------
button_update = QtGui.QPushButton('Update')
button_update.setStyleSheet("font-size:20px; font-family: Helvetica")
button_update.clicked.connect(on_press_button_update)
grid_layout.addWidget(button_update, 7, 0, 1, 1)
button_show_cross_correlograms = QtGui.QPushButton(
'Show Crosscorrelograms')
button_show_cross_correlograms.setStyleSheet(
"font-size:20px; font-family: Helvetica")
button_show_cross_correlograms.clicked.connect(
on_press_button_show_cross_correlograms)
grid_layout.addWidget(button_show_cross_correlograms, 7, 1, 1, 1)
tsne_color_scheme_combo_box = QtGui.QComboBox()
tsne_color_scheme_combo_box.setStyleSheet(
"font-size:20px; font-family: Helvetica")
tsne_color_scheme_combo_box.addItem('After sorting')
tsne_color_scheme_combo_box.addItem('Before sorting')
tsne_color_scheme_combo_box.activated.connect(
on_tsne_color_scheme_combo_box_change)
grid_layout.addWidget(tsne_color_scheme_combo_box, 7, 2, 1, 1)
tsne_filter_for_type_combo_box = QtGui.QComboBox()
tsne_filter_for_type_combo_box.setStyleSheet(
"font-size:20px; font-family: Helvetica")
tsne_filter_for_type_combo_box.addItem('All')
tsne_filter_for_type_combo_box.addItem('Single Unit')
tsne_filter_for_type_combo_box.addItem('Single Unit Contaminated')
tsne_filter_for_type_combo_box.addItem('Single Unit Putative')
tsne_filter_for_type_combo_box.addItem('Multi Unit')
tsne_filter_for_type_combo_box.addItem('Unspecified 1')
tsne_filter_for_type_combo_box.addItem('Unspecified 2')
tsne_filter_for_type_combo_box.addItem('Unspecified 3')
tsne_filter_for_type_combo_box.activated.connect(
on_tsne_filter_for_type_combo_box_change)
grid_layout.addWidget(tsne_filter_for_type_combo_box, 6, 2, 1, 1)
button_freeze_spikes = QtGui.QPushButton('Freeze selected spikes')
button_freeze_spikes.setStyleSheet(
"font-size:20px; font-family: Helvetica")
button_freeze_spikes.clicked.connect(on_press_button_freeze_spikes)
grid_layout.addWidget(button_freeze_spikes, 5, 3, 1, 1)
button_unfreeze_all = QtGui.QPushButton('Unfreeze all spikes')
button_unfreeze_all.setStyleSheet("font-size:20px; font-family: Helvetica")
button_unfreeze_all.clicked.connect(on_press_button_unfreeze_all)
grid_layout.addWidget(button_unfreeze_all, 6, 3, 1, 1)
button_remove_from_template = QtGui.QPushButton(
'Remove selected spikes from template')
button_remove_from_template.setStyleSheet(
"font-size:20px; font-family: Helvetica")
button_remove_from_template.clicked.connect(
on_press_button_remove_from_template)
grid_layout.addWidget(button_remove_from_template, 4, 6, 1, 1)
button_make_template = QtGui.QPushButton('Make new template from spikes')
button_make_template.setStyleSheet(
"font-size:20px; font-family: Helvetica")
button_make_template.clicked.connect(on_press_button_make_template)
grid_layout.addWidget(button_make_template, 5, 6, 1, 1)
# ----------------------------------
# Text Box -------------------------
selected_templates_text_box = QtWidgets.QLineEdit()
selected_templates_text_box.setReadOnly(True)
selected_templates_text_box.setWindowTitle('Selected Templates')
selected_templates_text_box.setStyleSheet(
"font-size:20px; font-family: Helvetica")
grid_layout.addWidget(selected_templates_text_box, 7, 3, 1, 2)
# ----------------------------------
if load_previous_dataset:
load_config()
main_window.show()
if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
sys.exit(app.exec_())
def __init__(self):
super(Stereography_window, self).__init__()
self.setWindowTitle('Tracker 5')
self.setMinimumWidth(1600)
self.setMinimumHeight(1000)
pg.setConfigOption('background', 'w')
pg.setConfigOption('foreground', 'k')
self.cur = QtGui.QCursor
# Create the QVBoxLayout that lays out the whole form
w = QtGui.QWidget()
self.layout = QtGui.QVBoxLayout(w)
self.setCentralWidget(w)
### top row, imageview widgets
self.images_hbox = QtGui.QHBoxLayout()
self.iml = pg.ImageView()
self.imr = pg.ImageView()
# self.iml.setMouseTracking(True)
# self.imr.setMouseTracking(True)
# self.imr_load = QtGui.QPushButton('Load right directory')
self.iml_load = QtGui.QPushButton('Load left Directory')
self.lfns, self.rfns = [], []
self.randim = n.random.randint(256, size=(640, 480))
self.iml.setImage(self.randim)
self.iml.setMinimumHeight(400)
self.iml.getHistogramWidget().setMaximumWidth(100)
self.iml.scene.sigMouseMoved.connect(self.lmouseMoved)
self.imr.setImage(self.randim)
self.imr.setMinimumHeight(400)
self.imr.getHistogramWidget().setMaximumWidth(100)
self.imr.scene.sigMouseMoved.connect(self.rmouseMoved)
self.images_hbox.addWidget(self.iml)
self.ltools = QtGui.QToolBar(self.iml)
self.ltools.setStyleSheet('QToolBar{spacing:0px;}')
self.loadl = self.ltools.addAction(QtGui.QIcon(), 'load', self.load)
self.ltools.show()
self.images_hbox.addWidget(self.imr)
self.rtools = QtGui.QToolBar(self.imr)
self.rtools.setStyleSheet('QToolBar{spacing:0px;}')
# self.loadr = self.rtools.addAction(QtGui.QIcon(), 'load', self.load_right)
self.rtools.show()
### middle row
# frame slider
self.frame_hbox = QtGui.QHBoxLayout()
self.frame_slider = QtGui.QSlider(QtCore.Qt.Horizontal)
self.frame_slider.setMinimum(1)
self.frame_slider.setMaximum(1)
self.frame_slider.valueChanged.connect(self.change_frame)
# self.frame_value = pg.ValueLabel()
self.frame_value = QtGui.QLabel('1/1')
self.frame_hbox.addWidget(self.frame_slider)
self.frame_hbox.addWidget(self.frame_value)
### bottom row
self.bottom_hbox = QtGui.QHBoxLayout()
# camera layout
self.camera_view = pg.PlotWidget()
self.camera_view.setAspectLocked(True)
self.camera_view.setMaximumWidth(400)
self.camera_view.setMaximumHeight(400)
self.tab = pg.TableWidget(editable=True, sortable=False)
self.tab.setData([[-14.13, 0, 14.13, 0.], [-15, 0, 15, 0.],
[53.5, 41.41, 53.5, 41.41]])
self.tab.setVerticalHeaderLabels(['pos', 'ang', 'fov'])
self.tab.setHorizontalHeaderLabels(
['cam1 x', 'cam1 y', 'cam2 x', 'cam2 y'])
self.tab.cellChanged.connect(self.update_camera_parameters)
self.update_camera_parameters(dist=100)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.camera_view)
vbox.addWidget(self.tab)
self.bottom_hbox.addItem(vbox)
# 3d plot
self.flight_view = gl.GLViewWidget()
self.flight_view.setBackgroundColor((0, 0, .5))
self.flight_view.setWindowTitle('pyqtgraph example: GLLinePlotItem')
self.flight_view.opts['distance'] = 40
gx = gl.GLGridItem(color=pg.mkColor([255, 0, 0, 255]))
gx.rotate(90, 0, 1, 0)
gx.translate(-10, 0, 0)
self.flight_view.addItem(gx)
gy = gl.GLGridItem()
gy.rotate(90, 1, 0, 0)
gy.translate(0, -10, 0)
self.flight_view.addItem(gy)
gz = gl.GLGridItem()
gz.translate(0, 0, -10)
self.flight_view.addItem(gz)
# self.flight_view.setSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Expanding)
# self.flight_view.show()
self.flight_lines = []
self.flight_pts = []
self.bottom_hbox.addWidget(self.flight_view)
### set the layout
self.layout.addLayout(self.images_hbox)
# self.layout.addWidget(self.frame_slider)
self.layout.addLayout(self.frame_hbox)
self.layout.addLayout(self.bottom_hbox)
### now the markers
self.num_cams = 2 #left and right
self.num_markers = 9 #1-9
self.num_frames = 1 #until we load a dir
self.marker_keys = [str(i + 1) for i in range(self.num_markers)
] # keyboard strings for each marker
self.shift_marker_keys = ['!', '@', '#', '$', '%', '^', '&', '*',
'('] # keyboard strings for each marker
alpha = 200
width = 4
self.colors = [
(255, 100, 100, alpha), #red
(100, 255, 100, alpha), #green
(60, 60, 255, alpha), #blue
(245, 245, 30, alpha), #yellow
(30, 245, 245, alpha), #cyan
(255, 0, 255, alpha), #magenta
(255, 195, 0, alpha), #orange
(150, 150, 255, alpha), #indigo
(215, 120, 255, alpha)
] #purple
# first the markers for the image
self.data_markers = [[], []]
for cam_ind in range(self.num_cams):
for marker_ind in range(self.num_markers):
# left
data_marker = pg.PolyLineROI([[0., 0.]
]) #roi with only a single point
data_marker.getHandles()[0].pen.setColor(
QtGui.QColor(*self.colors[marker_ind])
) #make each handle a different color
data_marker.getHandles()[0].pen.setWidth(width) #thicken lines
data_marker.sigRegionChanged.connect(self.marker_moved)
data_marker.hide() #initially invisible
self.data_markers[cam_ind].append(data_marker)
if cam_ind == 0: self.iml.addItem(data_marker)
if cam_ind == 1: self.imr.addItem(data_marker)
self.data = n.zeros(
(self.num_cams + 1, self.num_markers, 3, self.num_frames))
self.data[:, :, :, :] = n.NaN
# data positions interpolated
self.null_interp = InterpolatedUnivariateSpline([0, 0], [n.NaN, n.NaN],
k=1)
# self.data_interp = [[[self.null_interp]*2]*self.num_markers]*self.num_sides #[2 sides][num markers][x y] ##no t needed
self.data_interp = [[[self.null_interp for xy in range(2)]
for m in range(self.num_markers)]
for s in range(self.num_cams)]
# now the lines
for marker_ind in range(self.num_markers):
line = gl.GLLinePlotItem(pos=n.array([[0, 0, 0.], [1, 1, 1.]]),
color=pg.glColor(self.colors[marker_ind]),
width=2.,
antialias=True)
line.hide()
self.flight_lines.append(line)
self.flight_view.addItem(line)
pt = gl.GLScatterPlotItem(pos=n.array([[0, 0, 0.]]),
color=pg.glColor(
self.colors[marker_ind]),
size=10.)
pt.hide()
self.flight_pts.append(pt)
self.flight_view.addItem(pt)
def update_plots(self):
"""Checks the signal slots and changes the plotting attributes to be
evaluated by PlotWindow_lib.
This function coordinates the changing input from the signal slots and
updates the attributes that are parsed to the plotting lib functions.
update_plots() is either periodically called e.g. by the timer or once
on startup.
Args:
self: Object of the PlotWindow class.
Returns:
No return variable. The function operates on the given object.
"""
#print "PWL update_plots:", self.obj_parent.h5file
try:
self.ds = self.obj_parent.h5file[self.dataset_url]
except ValueError as e:
print(str(self.dataset_url)+": "+str(e))
return
self.ds_type = self.ds.attrs.get('ds_type', -1)
# The axis names are parsed to plot_view's Ui_Form class to label the UI selectors
x_ds_name = _get_name(_get_ds(self.ds, self.ds.attrs.get('x_ds_url', '')))
y_ds_name = _get_name(_get_ds(self.ds, self.ds.attrs.get('y_ds_url', '')))
z_ds_name = _get_name(_get_ds(self.ds, self.ds.attrs.get('z_ds_url', '')))
try:
if self.ds.attrs.get('xy_0', ''):
x_ds_name_view = _get_name(_get_ds(self.ds,_get_ds(self.ds, self.ds.attrs.get('xy_0', '').decode().split(':')[1]).attrs.get('x_ds_url', '')))
y_ds_name_view = _get_name(_get_ds(self.ds,_get_ds(self.ds, self.ds.attrs.get('xy_0', '').decode().split(':')[1]).attrs.get('y_ds_url', '')))
else:
raise AttributeError
except AttributeError:
x_ds_name_view = '_none_'
y_ds_name_view = '_none_'
selector_label = [x_ds_name, y_ds_name, z_ds_name, x_ds_name_view, y_ds_name_view]
## At first window creation the attributes are set to state zero.
if self._windowJustCreated:
# A few state variables:
self._onPlotTypeChanged = True
self._windowJustCreated = False
self.graphicsView = None
self.TraceValueChanged = False
self.TraceZValueChanged = False
self.TraceXValueChanged = False
self.TraceYValueChanged = False
self.VTraceZValueChanged = False
self.VTraceXValueChanged = False
self.VTraceYValueChanged = False
# the following calls rely on ds_type and setup the layout of the plot window.
self.setupUi(self,self.ds_type, selector_label)
window_title = str(self.dataset_url.split('/')[-1]) +" "+ str(self.DATA.filename)
self.setWindowTitle(window_title)
self._setDefaultView()
self._setup_signal_slots()
## We check here for the view type given by either default setting or
## user input. Creates the canvas and calls the associated plot
## function from the lib. For code constistence the variable names are
## the same in all view types.
try:
if self.view_type == view_types['1D-V']:
if not self.graphicsView or self._onPlotTypeChanged:
self._onPlotTypeChanged = False
self.graphicsView = pg.PlotWidget(name=self.dataset_url)
self.graphicsView.setObjectName(self.dataset_url)
self.addQvkMenu()
self.graphicsView.sceneObj.contextMenu[:0] = [self.qvkMenu]
self.gridLayout.addWidget(self.graphicsView,0,0)
_display_1D_view(self,self.graphicsView)
elif self.view_type == view_types['1D']:
if not self.graphicsView or self._onPlotTypeChanged:
self._onPlotTypeChanged = False
self.graphicsView = pg.PlotWidget(name=self.dataset_url)
self.graphicsView.setObjectName(self.dataset_url)
self.addQvkMenu()
self.graphicsView.sceneObj.contextMenu[:0] = [self.qvkMenu]
self.gridLayout.addWidget(self.graphicsView,0,0)
_display_1D_data(self,self.graphicsView)
elif self.view_type == view_types['2D']:
if not self.graphicsView or self._onPlotTypeChanged:
self._onPlotTypeChanged = False
self.graphicsView = ImageViewMplColorMaps(self.obj_parent, view = pg.PlotItem())
self.graphicsView.setObjectName(self.dataset_url)
self.addQvkMenu()
self.graphicsView.scene.contextMenu[:0] = [self.qvkMenu]
self.graphicsView.view.setAspectLocked(False)
self.gridLayout.addWidget(self.graphicsView,0,0)
self.linestyle_selector.setDisabled(True)
_display_2D_data(self,self.graphicsView)
elif self.view_type == view_types['table']:
if not self.graphicsView or self._onPlotTypeChanged:
self._onPlotTypeChanged = False
self.graphicsView = pg.TableWidget(sortable=False)
self.graphicsView.setWindowTitle(self.dataset_url+'_table')
self.graphicsView.setObjectName(self.dataset_url)
self.graphicsView.setFormat("%.6g")
self.gridLayout.addWidget(self.graphicsView,0,0)
_display_table(self,self.graphicsView)
elif self.view_type == view_types['txt']:
if not self.graphicsView or self._onPlotTypeChangeBox:
self._onPlotTypeChangeBox = False
self.graphicsView = QPlainTextEdit()
self.graphicsView.setObjectName(self.dataset_url)
self.gridLayout.addWidget(self.graphicsView,0,0)
self.graphicsView.clear()
_display_text(self,self.graphicsView)
else:
print("This should not be here: View Type:"+str(self.view_type))
except ValueError as e:
print("PlotWindow: Value Error; Dataset not yet available", self.dataset_url)
print(e)
cal["number_of_quads"]))
print("pulse_repetition_interval_hr_us={}".format(
cal["pulse_repetition_interval_hr_us"]))
n = 24072
w = 332
a = np.fromfile("/home/martin/sat-data/chunk0",
dtype=np.complex64,
count=((w) * (n))).reshape((
w,
n,
))
win = np.hamming(n)
import pyqtgraph as pg
from pyqtgraph.Qt import QtCore, QtGui
app = QtGui.QApplication([])
widget = pg.TableWidget(sortable=False)
widget.show()
widget.resize(500, 500)
widget.setWindowTitle("satellite data header")
font = QtGui.QFont()
font.setPointSize(5)
widget.setFont(font)
type_header = []
short_names = []
for c in list(df.columns):
example = df[c][0]
example_type = type(example)
short_name = "".join(map(lambda x: x[0], c.split("_")))
new_short_name = short_name
count = 0
while ((new_short_name in short_names)):
def __init__(self, mask, xsize=1000, ysize=1000, version='carpy'):
self.mask = mask
self.xsize = xsize
self.ysize = ysize
self.dW = 15.0
self.degree = 4
self.lines = Table.read('HeNeAr_check.dat', format='ascii')
lines_fit = np.copy(self.lines)
lines_fit = Table(lines_fit)
lines_fit['a'] = 0.0
lines_fit['b'] = 0.0
lines_fit['wave_fit'] = 0.0
lines_fit['amplitude'] = 0.0
lines_fit['sigma'] = 0.0
lines_fit['dW'] = 0.0
self.lines_fit = lines_fit
self.path = '{}_spec1D'.format(mask)
self.objects = Table.read('{}/{}_objects.fits'.format(
self.path, self.mask))
print(self.objects)
# Set the initial row number to zero
self.row = 1
self.nRows = len(self.objects)
self.smoothing = 1
# Get the GUI ready
self.app = QtGui.QApplication([]) # Always start by initializing Qt
self.widget = QtGui.QWidget() # Define a top-level widget
# Set the widget size
self.widget.resize(self.xsize, self.ysize)
# Set the background plotting widget
self.plot_solution = pg.PlotWidget()
self.plot_solution.getAxis('bottom').setPen(pg.mkPen('w', width=2))
self.plot_solution.getAxis('top').setPen(pg.mkPen('w', width=2))
self.plot_solution.getAxis('left').setPen(pg.mkPen('w', width=2))
self.plot_solution.getAxis('right').setPen(pg.mkPen('w', width=2))
self.plot_solution.getAxis('bottom').setStyle(tickLength=-15)
self.plot_solution.getAxis('top').setStyle(tickLength=-15)
self.plot_solution.getAxis('left').setStyle(tickLength=-15)
self.plot_solution.getAxis('right').setStyle(tickLength=-15)
self.plot_solution.showAxis('right')
self.plot_solution.showAxis('top')
self.plot_solution.setLabel('bottom', 'wavelength')
self.plot_solution.setLabel('left', 'dW [Å]')
# Set the 1D spectrum
self.plot_spec1D = pg.PlotWidget()
self.plot_spec1D.getAxis('bottom').setPen(pg.mkPen('w', width=2))
self.plot_spec1D.getAxis('top').setPen(pg.mkPen('w', width=2))
self.plot_spec1D.getAxis('left').setPen(pg.mkPen('w', width=2))
self.plot_spec1D.getAxis('right').setPen(pg.mkPen('w', width=2))
self.plot_spec1D.getAxis('bottom').setStyle(tickLength=-15)
self.plot_spec1D.getAxis('top').setStyle(tickLength=-15)
self.plot_spec1D.getAxis('left').setStyle(tickLength=-15)
self.plot_spec1D.getAxis('right').setStyle(tickLength=-15)
self.plot_spec1D.showAxis('right')
self.plot_spec1D.showAxis('top')
self.plot_spec1D.setLabel('bottom', 'Wavelength [Å]')
self.plot_spec1D.setLabel('bottom', 'arc flux')
self.plot_spec1D.setXLink(self.plot_solution)
self.mouse_x_spec1D = 0.0
self.mouse_y_spec1D = 0.0
self.mouse_x_solution = 0.0
self.mouse_y_solution = 0.0
# Setup the layout
self.layout = QtGui.QGridLayout()
self.widget.setLayout(self.layout)
# Add listeners
self.plot_spec1D.scene().sigMouseMoved.connect(self.mouseMoved_spec1D)
self.plot_spec1D.keyPressEvent = self.keypress_spec1D
self.plot_solution.scene().sigMouseMoved.connect(
self.mouseMoved_solution)
self.plot_solution.keyPressEvent = self.keypress_solution
self.objectsTable = pg.TableWidget(editable=False, sortable=False)
self.objectsTable.setFormat('%0.5f', 2)
self.setTable()
self.objectsTable.setSelectionBehavior(
QtGui.QAbstractItemView.SelectRows)
self.objectsTable.setSelectionMode(
QtGui.QAbstractItemView.SingleSelection)
self.objectsTable.doubleClicked.connect(self.goToObject)
self.linesTable_fit = pg.TableWidget(editable=False, sortable=False)
self.linesTable_fit.setFormat('%0.2f', 0)
self.linesTable_fit.setFormat('%0.2f', 1)
self.linesTable_fit.setFormat('%0.2f', 2)
self.linesTable_fit.setFormat('%0.2f', 3)
self.linesTable_fit.setFormat('%0.2f', 4)
self.linesTable_fit.setFormat('%0.2f', 5)
self.linesTable_fit.setFormat('%0.2f', 6)
self.setTable_lines()
# Add plot_bg to the layout
self.layout.addWidget(self.plot_solution, 0, 0)
self.layout.addWidget(self.linesTable_fit, 0, 1)
self.layout.addWidget(self.objectsTable, 1, 1)
self.layout.addWidget(self.plot_spec1D, 1, 0)
#self.layout.addWidget(self.comment_text, 4, 0)
self.layout.setColumnStretch(0, 0)
self.layout.setColumnStretch(0, 1)
self.layout.setColumnStretch(1, 0)
#self.layout.setColumnStretch(1, 1)
self.layout.setRowStretch(0, 0)
self.layout.setRowStretch(0, 1)
self.layout.setRowStretch(1, 0)
self.layout.setRowStretch(1, 1)
self.setSpec()
self.fitAll()
self.fitResiduals()
dW = self.lines_fit['dW'] - getpolyfit(self.lines_fit['wave'],
self.poly)
sigma_robust = stats.median_absolute_deviation(dW)
print('robust_sigma = {}'.format(sigma_robust))
index = np.where(np.abs(dW) > 5.0 * sigma_robust)
self.lines_fit['a'][index] = 0.0
self.lines_fit['b'][index] = 0.0
self.lines_fit['wave_fit'][index] = 0.0
self.lines_fit['amplitude'][index] = 0.0
self.lines_fit['sigma'][index] = 0.0
self.fitResiduals()
self.draw()
self.widget.show()
self.app.exec_()
def setupUi(self, MainWindow):
MainWindow.setObjectName("MainWindow")
MainWindow.resize(1261, 838)
MainWindow.setWindowTitle('Analytic Tool')
self.centralwidget = QtWidgets.QWidget(MainWindow)
self.centralwidget.setObjectName("centralwidget")
self.gridLayout = QtWidgets.QGridLayout(self.centralwidget)
self.gridLayout.setObjectName("gridLayout")
self.scrollArea = QtWidgets.QScrollArea(self.centralwidget)
self.scrollArea.setFrameShape(QtWidgets.QFrame.NoFrame)
self.scrollArea.setWidgetResizable(True)
self.scrollArea.setObjectName("scrollArea")
self.scrollAreaWidgetContents = QtWidgets.QWidget()
self.scrollAreaWidgetContents.setGeometry(QtCore.QRect(0, 0, 541, 765))
self.scrollAreaWidgetContents.setObjectName("scrollAreaWidgetContents")
self.gridLayout_2 = QtWidgets.QGridLayout(
self.scrollAreaWidgetContents)
self.gridLayout_2.setObjectName("gridLayout_2")
self.gridLayout_2.setColumnMinimumWidth(4, 1)
self.rowLabel = QtWidgets.QLabel(self.scrollAreaWidgetContents)
self.rowLabel.setLayoutDirection(QtCore.Qt.LeftToRight)
self.rowLabel.setStyleSheet(
"background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(181, 181, 181, 255), stop:1 rgba(255, 255, 255, 255));"
)
self.rowLabel.setFrameShape(QtWidgets.QFrame.NoFrame)
self.rowLabel.setScaledContents(False)
self.rowLabel.setObjectName("rowLabel")
self.rowLabel.setText("Rows")
self.gridLayout_2.addWidget(self.rowLabel, 4, 1)
self.rowListWidget = QtWidgets.QListWidget(
self.scrollAreaWidgetContents)
self.rowListWidget.setObjectName("rowListWidget")
self.rowListWidget.setDefaultDropAction(QtCore.Qt.MoveAction)
self.rowListWidget.setDragDropMode(
QtWidgets.QAbstractItemView.DragDrop)
self.rowListWidget.currentItemChanged.connect(self.displayRowsFilter)
self.gridLayout_2.addWidget(self.rowListWidget, 5, 1)
self.columnLabel = QtWidgets.QLabel(self.scrollAreaWidgetContents)
self.columnLabel.setLayoutDirection(QtCore.Qt.LeftToRight)
self.columnLabel.setStyleSheet(
"background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(181, 181, 181, 255), stop:1 rgba(255, 255, 255, 255));"
)
self.columnLabel.setFrameShape(QtWidgets.QFrame.NoFrame)
self.columnLabel.setScaledContents(False)
self.columnLabel.setObjectName("columnLabel")
self.columnLabel.setText("Columns")
self.gridLayout_2.addWidget(self.columnLabel, 2, 1, 1, 1)
self.columnListWidget = QtWidgets.QListWidget(
self.scrollAreaWidgetContents)
self.columnListWidget.setObjectName("columnListWidget")
self.columnListWidget.setDefaultDropAction(QtCore.Qt.MoveAction)
self.columnListWidget.setDragDropMode(
QtWidgets.QAbstractItemView.DragDrop)
self.columnListWidget.currentItemChanged.connect(
self.displayColumnFilter)
self.gridLayout_2.addWidget(self.columnListWidget, 3, 1)
self.filterLabel = QtWidgets.QLabel(self.scrollAreaWidgetContents)
self.filterLabel.setLayoutDirection(QtCore.Qt.LeftToRight)
self.filterLabel.setStyleSheet(
"background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(181, 181, 181, 255), stop:1 rgba(255, 255, 255, 255));"
)
self.filterLabel.setFrameShape(QtWidgets.QFrame.NoFrame)
self.filterLabel.setScaledContents(False)
self.filterLabel.setObjectName("filterLabel")
self.filterLabel.setText("Filter")
self.gridLayout_2.addWidget(self.filterLabel, 0, 1)
self.filterListWidget = QtWidgets.QListWidget(
self.scrollAreaWidgetContents)
self.filterListWidget.setObjectName("filterListWidget")
self.gridLayout_2.addWidget(self.filterListWidget, 1, 1)
self.sheetLabel = QtWidgets.QLabel(self.scrollAreaWidgetContents)
self.sheetLabel.setLayoutDirection(QtCore.Qt.LeftToRight)
self.sheetLabel.setStyleSheet(
"background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(181, 181, 181, 255), stop:1 rgba(255, 255, 255, 255));"
)
self.sheetLabel.setFrameShape(QtWidgets.QFrame.NoFrame)
self.sheetLabel.setScaledContents(False)
self.sheetLabel.setObjectName("sheetLabel")
self.sheetLabel.setText("Sheets")
self.gridLayout_2.addWidget(self.sheetLabel, 0, 0)
# Set sheet list widget
self.sheetListWidget = QtWidgets.QListWidget(
self.scrollAreaWidgetContents)
self.sheetListWidget.setObjectName("sheetList")
self.sheetListWidget.itemActivated.connect(
self.displayDimensionsMeasurements)
self.gridLayout_2.addWidget(self.sheetListWidget, 1, 0)
self.measurementLabel = QtWidgets.QLabel(self.scrollAreaWidgetContents)
self.measurementLabel.setLayoutDirection(QtCore.Qt.LeftToRight)
self.measurementLabel.setStyleSheet(
"background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(181, 181, 181, 255), stop:1 rgba(255, 255, 255, 255));"
)
self.measurementLabel.setFrameShape(QtWidgets.QFrame.NoFrame)
self.measurementLabel.setScaledContents(False)
self.measurementLabel.setObjectName("measurementLabel")
self.measurementLabel.setText("Measurements")
self.gridLayout_2.addWidget(self.measurementLabel, 4, 0)
self.measurementWidget = QtWidgets.QListWidget(
self.scrollAreaWidgetContents)
self.measurementWidget.setObjectName("measurementsList")
self.measurementWidget.setDefaultDropAction(QtCore.Qt.MoveAction)
self.measurementWidget.setDragDropMode(
QtWidgets.QAbstractItemView.DragDrop)
self.gridLayout_2.addWidget(self.measurementWidget, 5, 0)
self.dimensionLabel = QtWidgets.QLabel(self.scrollAreaWidgetContents)
self.dimensionLabel.setLayoutDirection(QtCore.Qt.LeftToRight)
self.dimensionLabel.setStyleSheet(
"\n"
"background-color: qlineargradient(spread:pad, x1:0, y1:0, x2:1, y2:0, stop:0 rgba(181, 181, 181, 255), stop:1 rgba(255, 255, 255, 255));"
)
self.dimensionLabel.setFrameShape(QtWidgets.QFrame.NoFrame)
self.dimensionLabel.setScaledContents(False)
self.dimensionLabel.setObjectName("dimensionLabel")
self.dimensionLabel.setText("Dimensions")
self.gridLayout_2.addWidget(self.dimensionLabel, 2, 0)
self.dimensionWidget = QtWidgets.QListWidget(
self.scrollAreaWidgetContents)
self.dimensionWidget.setObjectName("dimensionList")
self.dimensionWidget.setDefaultDropAction(QtCore.Qt.MoveAction)
self.dimensionWidget.setDragDropMode(
QtWidgets.QAbstractItemView.DragDrop)
self.gridLayout_2.addWidget(self.dimensionWidget, 3, 0)
self.scrollArea.setWidget(self.scrollAreaWidgetContents)
self.gridLayout.addWidget(self.scrollArea, 0, 0)
self.scrollArea_2 = QtWidgets.QScrollArea(self.centralwidget)
self.scrollArea_2.setFrameShape(QtWidgets.QFrame.NoFrame)
self.scrollArea_2.setWidgetResizable(True)
self.scrollArea_2.setObjectName("scrollArea_2")
self.scrollAreaWidgetContents_2 = QtWidgets.QWidget()
self.scrollAreaWidgetContents_2.setGeometry(
QtCore.QRect(0, 0, 342, 765))
self.scrollAreaWidgetContents_2.setObjectName(
"scrollAreaWidgetContents_2")
self.gridLayout_3 = QtWidgets.QGridLayout(
self.scrollAreaWidgetContents_2)
self.gridLayout_3.setObjectName("gridLayout_3")
self.continuousChart = QtWidgets.QToolButton(
self.scrollAreaWidgetContents_2)
self.continuousChart.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Expanding)
self.continuousChart.setToolButtonStyle(
3) # Set text position under icon
self.continuousChart.setText("Continuous")
continuousChartIcon = QtGui.QIcon()
continuousChartIcon.addPixmap(
QtGui.QPixmap(":/resource/continuousChart.svg"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.continuousChart.setIcon(continuousChartIcon)
self.continuousChart.setIconSize(QtCore.QSize(70, 70))
self.continuousChart.setObjectName("continuousChart")
self.gridLayout_3.addWidget(self.continuousChart, 4, 0)
self.blockChart = QtWidgets.QToolButton(
self.scrollAreaWidgetContents_2)
self.blockChart.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Expanding)
self.blockChart.setToolButtonStyle(3) # Set text position under icon
self.blockChart.setText("Block")
blockChartIcon = QtGui.QIcon()
blockChartIcon.addPixmap(QtGui.QPixmap(":/resource/blockChart.svg"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.blockChart.setIcon(blockChartIcon)
self.blockChart.setIconSize(QtCore.QSize(70, 70))
self.blockChart.setObjectName("blockChart")
self.gridLayout_3.addWidget(self.blockChart, 2, 0)
self.horizontalBarChart = QtWidgets.QToolButton(
self.scrollAreaWidgetContents_2)
self.horizontalBarChart.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Expanding)
self.horizontalBarChart.setToolButtonStyle(
3) # Set text position under icon
self.horizontalBarChart.setText("Horizontal Bar")
horizontalBarIcon = QtGui.QIcon()
horizontalBarIcon.addPixmap(
QtGui.QPixmap(":/resource/horizontalBarChart.svg"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.horizontalBarChart.setIcon(horizontalBarIcon)
self.horizontalBarChart.setIconSize(QtCore.QSize(70, 70))
self.horizontalBarChart.setObjectName("horizontalBarChart")
self.gridLayout_3.addWidget(self.horizontalBarChart, 3, 0)
self.pieChart = QtWidgets.QToolButton(self.scrollAreaWidgetContents_2)
self.pieChart.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Expanding)
self.pieChart.setToolButtonStyle(3) # Set text position under icon
self.pieChart.setText("Pie Chart")
pieChartIcon = QtGui.QIcon()
pieChartIcon.addPixmap(QtGui.QPixmap(":/resource/pieChart.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.pieChart.setIcon(pieChartIcon)
self.pieChart.setIconSize(QtCore.QSize(70, 70))
self.pieChart.setObjectName("pieChart")
self.gridLayout_3.addWidget(self.pieChart, 0, 0)
self.circleChart = QtWidgets.QToolButton(
self.scrollAreaWidgetContents_2)
self.circleChart.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Expanding)
self.circleChart.setToolButtonStyle(3) # Set text position under icon
self.circleChart.setText("Circle")
circleChartIcon = QtGui.QIcon()
circleChartIcon.addPixmap(QtGui.QPixmap(":/resource/circleView.svg"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.circleChart.setIcon(circleChartIcon)
self.circleChart.setIconSize(QtCore.QSize(70, 70))
self.circleChart.setObjectName("circleChart")
self.gridLayout_3.addWidget(self.circleChart, 5, 0)
self.table = QtWidgets.QToolButton(self.scrollAreaWidgetContents_2)
self.table.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Expanding)
self.table.setToolButtonStyle(3) # Set text position under icon
self.table.setText("Table")
tableIcon = QtGui.QIcon()
tableIcon.addPixmap(QtGui.QPixmap(":/resource/tableChart.svg"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.table.setIcon(tableIcon)
self.table.setIconSize(QtCore.QSize(70, 70))
self.table.setObjectName("table")
self.gridLayout_3.addWidget(self.table, 1, 0)
self.histogram = QtWidgets.QToolButton(self.scrollAreaWidgetContents_2)
self.histogram.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Expanding)
self.histogram.setToolButtonStyle(3) # Set text position under icon
self.histogram.setText("Histogram")
histrogramIcon = QtGui.QIcon()
histrogramIcon.addPixmap(
QtGui.QPixmap(":/resource/histrogramChart.svg"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.histogram.setIcon(histrogramIcon)
self.histogram.setIconSize(QtCore.QSize(70, 70))
self.histogram.setObjectName("histogram")
self.gridLayout_3.addWidget(self.histogram, 0, 1)
self.scatter = QtWidgets.QToolButton(self.scrollAreaWidgetContents_2)
scatterIcon = QtGui.QIcon()
self.scatter.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Expanding)
self.scatter.setToolButtonStyle(3) # Set text position under icon
self.scatter.setText("Scatter")
scatterIcon.addPixmap(QtGui.QPixmap(":/resource/scatterChart.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.scatter.setIcon(scatterIcon)
self.scatter.setIconSize(QtCore.QSize(70, 70))
self.scatter.setObjectName("scatter")
self.gridLayout_3.addWidget(self.scatter, 1, 1)
self.stackBarChart = QtWidgets.QToolButton(
self.scrollAreaWidgetContents_2)
self.stackBarChart.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Expanding)
self.stackBarChart.setToolButtonStyle(
3) # Set text position under icon
self.stackBarChart.setText("Stack Bar")
stackBarIcon = QtGui.QIcon()
stackBarIcon.addPixmap(QtGui.QPixmap(":/resource/stackBarChart.svg"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.stackBarChart.setIcon(stackBarIcon)
self.stackBarChart.setIconSize(QtCore.QSize(70, 70))
self.stackBarChart.setObjectName("stackBarChart")
self.gridLayout_3.addWidget(self.stackBarChart, 2, 1)
self.sidebysideBarChart = QtWidgets.QToolButton(
self.scrollAreaWidgetContents_2)
self.sidebysideBarChart.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Expanding)
self.sidebysideBarChart.setToolButtonStyle(
3) # Set text position under icon
self.sidebysideBarChart.setText("Side By Side")
sidebysideIcon = QtGui.QIcon()
sidebysideIcon.addPixmap(
QtGui.QPixmap(":/resource/sidebysideBarChart.png"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.sidebysideBarChart.setIcon(sidebysideIcon)
self.sidebysideBarChart.setIconSize(QtCore.QSize(70, 70))
self.sidebysideBarChart.setObjectName("sidebysideBarChart")
self.gridLayout_3.addWidget(self.sidebysideBarChart, 3, 1)
self.bubbleChart = QtWidgets.QToolButton(
self.scrollAreaWidgetContents_2)
self.bubbleChart.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Expanding)
self.bubbleChart.setToolButtonStyle(3) # Set text position under icon
self.bubbleChart.setText("Bubble")
bubbleChartIcon = QtGui.QIcon()
bubbleChartIcon.addPixmap(QtGui.QPixmap(":/resource/bubbleChart.svg"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.bubbleChart.setIcon(bubbleChartIcon)
self.bubbleChart.setIconSize(QtCore.QSize(70, 70))
self.bubbleChart.setObjectName("bubbleChart")
self.gridLayout_3.addWidget(self.bubbleChart, 4, 1)
self.dualChart = QtWidgets.QToolButton(self.scrollAreaWidgetContents_2)
self.dualChart.setSizePolicy(QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Expanding)
self.dualChart.setToolButtonStyle(3) # Set text position under icon
self.dualChart.setText("Dual Chart")
dualChartIcon = QtGui.QIcon()
dualChartIcon.addPixmap(QtGui.QPixmap(":/resource/dualChart.svg"),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.dualChart.setIcon(dualChartIcon)
self.dualChart.setIconSize(QtCore.QSize(70, 70))
self.dualChart.setObjectName("dualChart")
self.gridLayout_3.addWidget(self.dualChart, 5, 1)
self.scrollArea_2.setWidget(self.scrollAreaWidgetContents_2)
self.gridLayout.addWidget(self.scrollArea_2, 0, 2)
self.tabWidget = QtWidgets.QTabWidget(self.centralwidget)
self.tabWidget.setBaseSize(QtCore.QSize(2000, 2000))
self.tabWidget.setObjectName("tabWidget")
self.chartTab = QtWidgets.QWidget()
self.chartTab.setObjectName("chartTab")
self.plotLayout = QtWidgets.QVBoxLayout()
self.plotWidget = pg.PlotWidget(name='Plot')
self.plotLayout.addWidget(self.plotWidget)
self.chartTab.setLayout(self.plotLayout)
self.tabWidget.addTab(self.chartTab, "")
self.tabWidget.setTabText(self.tabWidget.indexOf(self.chartTab),
"Chart")
self.tableTab = QtWidgets.QWidget()
self.tableTab.setObjectName("tableTab")
self.tableLayout = QtWidgets.QVBoxLayout()
self.tableWidget = pg.TableWidget()
self.tableLayout.addWidget(self.tableWidget)
self.tableTab.setLayout(self.tableLayout)
self.tabWidget.addTab(self.tableTab, "")
self.gridLayout.addWidget(self.tabWidget, 0, 1)
self.tabWidget.setTabText(self.tabWidget.indexOf(self.chartTab),
"Chart")
self.tabWidget.setTabText(self.tabWidget.indexOf(self.tableTab),
"Table")
MainWindow.setCentralWidget(self.centralwidget)
self.menubar = QtWidgets.QMenuBar(MainWindow)
self.menubar.setGeometry(QtCore.QRect(0, 0, 1261, 26))
self.menubar.setObjectName("menubar")
MainWindow.setMenuBar(self.menubar)
self.statusbar = QtWidgets.QStatusBar(MainWindow)
self.statusbar.setObjectName("statusbar")
MainWindow.setStatusBar(self.statusbar)
self.menuFile = QtWidgets.QMenu(self.menubar)
self.menuFile.setObjectName("menuFile")
self.menuFile.setTitle("File")
self.actionOpen = QtWidgets.QAction(MainWindow)
self.actionOpen.setObjectName("actionImport")
self.actionOpen.setText("Open")
self.actionOpen.setShortcut("Ctrl+O")
self.actionOpen.triggered.connect(self.openFileDialog)
self.actionImport = QtWidgets.QAction(MainWindow)
self.actionImport.setObjectName("actionImport")
self.actionImport.setText("Import")
self.actionImport.setShortcut("Ctrl+O")
self.actionImport.triggered.connect(self.openFileDialog)
self.actionSave = QtWidgets.QAction(MainWindow)
self.actionSave.setObjectName("actionSave")
self.actionSave.setText("Save")
self.actionSave.setShortcut("Ctrl+S")
self.actionSave.triggered.connect(self.saveFileDialog)
self.actionExport = QtWidgets.QAction(MainWindow)
self.actionExport.setObjectName("actionExport")
self.actionExport.setText("Export")
self.actionExport.setShortcut("Ctrl+E")
self.actionExport.triggered.connect(self.exportFileDialog)
self.menuFile.addAction(self.actionOpen)
self.menuFile.addAction(self.actionImport)
self.menuFile.addAction(self.actionSave)
self.menuFile.addAction(self.actionExport)
self.menubar.addAction(self.menuFile.menuAction())
self.tabWidget.setCurrentIndex(0)
QtCore.QMetaObject.connectSlotsByName(MainWindow)
curve4 = fig2.plot(pen=(120,120,20),name="M4")
curve5 = fig2.plot(pen=(160, 80,20),name="M5")
curve6 = fig2.plot(pen=(200, 40,20),name="M6")
curve1.setData(pData[0])
curve2.setData(pData[1])
curve3.setData(pData[2])
curve4.setData(pData[3])
curve5.setData(pData[4])
curve6.setData(pData[5])
textMax = pg.TextItem(html='<div style="text-align: center;"><span style="color: #FF0; font-size: 12pt;">Presione Inicio</span></div>', anchor=(-0.3,1), angle=0, fill=(0, 0, 255, 100))
fig2.addItem(textMax)
tab1 = pg.TableWidget()
items = ["M1(mm)","M2(mm)","M3(mm)","M4(mm)","M5(mm)","M6(mm)","Fx(Kg)"]
tab1.setRowCount(1000)
tab1.setColumnCount(7)
tab1.setHorizontalHeaderLabels(items)
softlabel = QtGui.QLabel('<div style="text-align: center;"><span style="color: #FFF; font-size: 14pt;">Ensayo de Compresion Axial y Diagonal</span></div>')
loadlabel = QtGui.QLabel('<div style="text-align: center;"><span style="color: #FF0; font-size: 16pt;">Carga: %s Kg</span></div>'%(uData[6]))
microlabel = QtGui.QLabel('<div style="text-align: center;"><span style="color: #FF0; font-size: 16pt;">Deformaciones: M1: %s, M2: %s, M3: %s, M4: %s, M5: %s, M6: %s,</span></div>'%(uData[0],uData[1],uData[2],uData[3],uData[4],uData[5]))
plotBtn = QtGui.QPushButton('Plot')
portlabel = QtGui.QLabel("Puerto:")
portSel = QtGui.QComboBox()
def test_TableWidget():
w = pg.TableWidget(sortable=False)
# Test all input data types
w.setData(listOfTuples)
assertTableData(w, listOfTuples)
w.setData(listOfLists)
assertTableData(w, listOfTuples)
w.setData(plainArray)
assertTableData(w, listOfTuples)
w.setData(recordArray)
assertTableData(w, listOfTuples)
w.setData(dictOfLists)
assertTableData(w, transposed)
w.appendData(dictOfLists)
assertTableData(w, transposed * 2)
w.setData(listOfDicts)
assertTableData(w, listOfTuples)
w.appendData(listOfDicts)
assertTableData(w, listOfTuples * 2)
# Test sorting
w.setData(listOfTuples)
w.sortByColumn(0, pg.QtCore.Qt.AscendingOrder)
assertTableData(w, sorted(listOfTuples, key=lambda a: a[0]))
w.sortByColumn(1, pg.QtCore.Qt.AscendingOrder)
assertTableData(w, sorted(listOfTuples, key=lambda a: a[1]))
w.sortByColumn(2, pg.QtCore.Qt.AscendingOrder)
assertTableData(w, sorted(listOfTuples, key=lambda a: a[2]))
w.setSortMode(1, 'text')
w.sortByColumn(1, pg.QtCore.Qt.AscendingOrder)
assertTableData(w, sorted(listOfTuples, key=lambda a: str(a[1])))
w.setSortMode(1, 'index')
w.sortByColumn(1, pg.QtCore.Qt.AscendingOrder)
assertTableData(w, listOfTuples)
# Test formatting
item = w.item(0, 2)
assert item.text() == ('%0.3g' % item.value)
w.setFormat('%0.6f')
assert item.text() == ('%0.6f' % item.value)
w.setFormat('X%0.7f', column=2)
assert isinstance(item.value, float)
assert item.text() == ('X%0.7f' % item.value)
# test setting items that do not exist yet
w.setFormat('X%0.7f', column=3)
# test append uses correct formatting
w.appendRow(('x', 10, 7.3))
item = w.item(w.rowCount() - 1, 2)
assert isinstance(item.value, float)
assert item.text() == ('X%0.7f' % item.value)
# test reset back to defaults
w.setFormat(None, column=2)
assert isinstance(item.value, float)
assert item.text() == ('%0.6f' % item.value)
w.setFormat(None)
assert isinstance(item.value, float)
assert item.text() == ('%0.3g' % item.value)
# test function formatter
def fmt(item):
if isinstance(item.value, float):
return "%d %f" % (item.index, item.value)
else:
return pg.asUnicode(item.value)
w.setFormat(fmt)
assert isinstance(item.value, float)
assert isinstance(item.index, int)
assert item.text() == ("%d %f" % (item.index, item.value))
assert isinstance(item.value, float)
assert item.text() == ('X%0.7f' % item.value)
# test reset back to defaults
w.setFormat(None, column=2)
assert isinstance(item.value, float)
assert item.text() == ('%0.6f' % item.value)
w.setFormat(None)
assert isinstance(item.value, float)
assert item.text() == ('%0.3g' % item.value)
# test function formatter
def fmt(item):
if isinstance(item.value, float):
return "%d %f" % (item.index, item.value)
else:
return pg.asUnicode(item.value)
w.setFormat(fmt)
assert isinstance(item.value, float)
assert isinstance(item.index, int)
assert item.text() == ("%d %f" % (item.index, item.value))
if __name__ == '__main__':
w = pg.TableWidget(editable=True)
w.setData(listOfTuples)
w.resize(600, 600)
w.show()
def update_plots(self):
""" This brings up everything and is therefore the main function.
Update Plots is either periodically called e.g. by the timer or once on startup. """
#print "PWL update_plots:", self.obj_parent.h5file
self.ds = self.obj_parent.h5file[self.dataset_url]
self.ds_type = self.ds.attrs.get('ds_type', -1)
if self._windowJustCreated:
# A few state variables:
self._onPlotTypeChanged = True
self._windowJustCreated = False
self.graphicsView = None
self.TraceValueChanged = False
self.TraceZValueChanged = False
self.TraceXValueChanged = False
self.TraceYValueChanged = False
self.VTraceZValueChanged = False
self.VTraceXValueChanged = False
self.VTraceYValueChanged = False
# the following calls rely on ds_type and setup the layout of the plot window.
self.setupUi(self, self.ds_type)
window_title = str(self.dataset_url.split('/')[-1]) + " " + str(
self.DATA.filename)
self.setWindowTitle(window_title)
self._setDefaultView()
self._setup_signal_slots()
try:
if self.view_type == view_types['1D-V']:
if not self.graphicsView or self._onPlotTypeChanged:
self._onPlotTypeChanged = False
self.graphicsView = pg.PlotWidget(name=self.dataset_url)
self.graphicsView.setObjectName(self.dataset_url)
self.addQvkMenu(self.graphicsView.plotItem.getMenu())
self.gridLayout.addWidget(self.graphicsView, 0, 0)
_display_1D_view(self, self.graphicsView)
elif self.view_type == view_types['1D']:
if not self.graphicsView or self._onPlotTypeChanged:
self._onPlotTypeChanged = False
self.graphicsView = pg.PlotWidget(name=self.dataset_url)
self.graphicsView.setObjectName(self.dataset_url)
self.addQvkMenu(self.graphicsView.plotItem.getMenu())
self.gridLayout.addWidget(self.graphicsView, 0, 0)
_display_1D_data(self, self.graphicsView)
elif self.view_type == view_types['2D']:
if not self.graphicsView or self._onPlotTypeChanged:
self._onPlotTypeChanged = False
self.graphicsView = pg.ImageView(self.obj_parent,
view=pg.PlotItem())
self.graphicsView.setObjectName(self.dataset_url)
self.addQvkMenu(self.graphicsView.view.getMenu())
#self.addQvkMenu(self..graphicsView.getImageItem().getMenu())
self.graphicsView.view.setAspectLocked(False)
self.gridLayout.addWidget(self.graphicsView, 0, 0)
_display_2D_data(self, self.graphicsView)
elif self.view_type == view_types['table']:
if not self.graphicsView or self._onPlotTypeChanged:
self._onPlotTypeChanged = False
self.graphicsView = pg.TableWidget(sortable=False)
self.graphicsView.setWindowTitle(self.dataset_url +
'_table')
self.graphicsView.setObjectName(self.dataset_url)
self.gridLayout.addWidget(self.graphicsView, 0, 0)
_display_table(self, self.graphicsView)
elif self.view_type == view_types['txt']:
if not self.graphicsView or self._onPlotTypeChangeBox:
self._onPlotTypeChangeBox = False
self.graphicsView = QPlainTextEdit()
self.graphicsView.setObjectName(self.dataset_url)
self.gridLayout.addWidget(self.graphicsView, 0, 0)
#self.graphicsView.setObjectName(self.dataset_url)
self.gridLayout.addWidget(self.graphicsView, 0, 0)
self.graphicsView.clear()
_display_text(self, self.graphicsView)
else:
print("This should not be here: View Type:" +
str(self.view_type))
except ValueError as e:
print("PlotWindow: Value Error; Dataset not yet available",
self.dataset_url)
print(e)
def __init__(self, group, parent=None):
super(GroupAnalyzer,
self).__init__(parent) ## Create window with ImageView widget
# self=QWidget()
self.group = group
nPuffs = len(self.group.puffs)
self.offsets = [puff.kinetics['t_start'] for puff in self.group.puffs]
cmap = matplotlib.cm.gist_rainbow
self.colors = [cmap(int(i * 255. / nPuffs)) for i in np.arange(nPuffs)]
self.colors = [
tuple([int(c * 255) for c in col]) for col in self.colors
]
self.setGeometry(QRect(1065, 121, 749, 948))
self.setWindowTitle('Group Analyzer')
self.hbox = QGridLayout()
self.setLayout(self.hbox)
self.area = DockArea()
self.hbox.addWidget(self.area)
self.d1 = Dock("Measured amplitude over time", size=(500, 300))
self.d2 = Dock("Variables", size=(146, 400))
self.d3 = Dock("Event View", size=(500, 400))
self.d4 = Dock("X over time", size=(500, 300))
self.d5 = Dock("Y over time", size=(500, 300))
self.d6 = Dock("Fitted amplitude over time", size=(500, 300))
self.d7 = Dock("Sigma over time", size=(500, 300))
self.d8 = Dock("3D fit", size=(500, 400))
self.d9 = Dock("Puff Data", size=(500, 400))
self.area.addDock(
self.d6, 'left'
) ## place d1 at left edge of dock area (it will fill the whole space since there are no other docks yet)
self.area.addDock(self.d2, 'right',
self.d6) ## place d2 at right edge of dock area
self.area.addDock(self.d8, 'bottom')
self.area.addDock(self.d9, 'below', self.d8)
self.area.addDock(self.d3, 'above',
self.d8) ## place d3 at bottom edge of d1
self.area.addDock(self.d4, 'below', self.d6)
self.area.addDock(self.d5, 'below', self.d4)
self.area.addDock(self.d7, 'below', self.d5)
self.area.addDock(self.d1, 'above', self.d6)
self.p1 = pg.PlotWidget(title="Measured amplitude over time")
self.d1.addWidget(self.p1)
self.p2 = pg.PlotWidget(title="Fitted amplitude over time")
self.d6.addWidget(self.p2)
self.p3 = pg.PlotWidget(title="Fitted X over time")
self.d4.addWidget(self.p3)
self.p4 = pg.PlotWidget(title="Fitted Y over time")
self.d5.addWidget(self.p4)
self.p5 = pg.PlotWidget(title="Fitted Sigma over time")
self.d7.addWidget(self.p5)
self.puff_3D = puff_3D()
self.d8.addWidget(self.puff_3D)
self.table = pg.TableWidget()
self.d9.addWidget(self.table)
self.formlayout = QFormLayout()
self.puffCheckBoxes = [QCheckBox() for puff in group.puffs]
for i in np.arange(nPuffs):
self.puffCheckBoxes[i].setChecked(True)
self.puffCheckBoxes[i].stateChanged.connect(self.replot)
self.formlayout.addRow('Puff ' + str(i), self.puffCheckBoxes[i])
self.alignAverageCheckBox = QCheckBox()
self.formlayout.addRow('Align Average', self.alignAverageCheckBox)
self.currentPuff = QComboBox()
for i in np.arange(nPuffs):
self.currentPuff.addItem('Puff ' + str(i))
self.currentPuff.currentIndexChanged.connect(self.changeCurrentPuff)
self.formlayout.addRow('Current Puff', self.currentPuff)
# self.exportButton=QPushButton("Export")
# self.exportButton.clicked.connect(self.export)
# self.formlayout.addWidget(self.exportButton)
self.formWidget = QWidget()
self.formWidget.setLayout(self.formlayout)
self.d2.addWidget(self.formWidget)
self.imageview = pg.ImageView()
puff = self.group.puffs[self.currentPuff.currentIndex()]
self.bounds = np.copy(puff.bounds)
self.bounds[0, 0] = puff.kinetics['before']
self.bounds[0, 1] = puff.kinetics['after']
bb = self.bounds
self.I = self.group.puffs[0].puffs.normalized_window.image[
bb[0][0]:bb[0][1] + 1, bb[1][0]:bb[1][1] + 1,
bb[2][0]:bb[2][1] + 1]
self.imageview.setImage(self.I)
self.addedItems = []
self.sigTimeChanged.connect(self.updateTime)
self.imageview.timeLine.sigPositionChanged.connect(self.updateindex)
self.d3.addWidget(self.imageview)
self.params = []
self.I_fits = []
for puff in self.group.puffs:
param, I_fit = self.getParamsOverTime(puff)
self.params.append(param)
self.I_fits.append(I_fit)
self.previousframe = -1
self.replot()
self.updatePuffTable()
self.updateTime(0)
self.show()
# -*- coding: utf-8 -*-
"""
Simple demonstration of TableWidget, which is an extension of QTableWidget
that automatically displays a variety of tabluar data formats.
"""
import initExample ## Add path to library (just for examples; you do not need this)
import pyqtgraph as pg
from pyqtgraph.Qt import QtCore, QtGui
import numpy as np
app = QtGui.QApplication([])
w = pg.TableWidget()
w.show()
w.resize(500,500)
w.setWindowTitle('pyqtgraph example: TableWidget')
data = np.array([
(1, 1.6, 'x'),
(3, 5.4, 'y'),
(8, 12.5, 'z'),
(443, 1e-12, 'w'),
], dtype=[('Column 1', int), ('Column 2', float), ('Column 3', object)])
w.setData(data)
## Start Qt event loop unless running in interactive mode or using pyside.
if __name__ == '__main__':
def initUI(self):
# self.area = DockArea()
# self.setCentralWidget(self.area)
# self.resize(1000,500)
self.resize(self.screen_size.width(), self.screen_size.height())
self.setWindowTitle('Display widget')
self.setWindowIcon(QIcon('DigitalPulses\display_image_icon.jpg'))
self.setWindowState(Qt.WindowMaximized)
self.d1 = da.Dock("Image",
size=(self.screen_size.width() / 2,
self.screen_size.height()
)) ## give this dock the minimum possible size
self.d3 = da.Dock("Number of atoms",
size=(self.screen_size.width() / 2,
self.screen_size.height() / 3))
self.d2 = da.Dock("Image data",
size=(self.screen_size.width() / 2,
self.screen_size.height() / 3))
self.d4 = da.Dock("Cloud width",
size=(self.screen_size.width() / 2,
self.screen_size.height() / 3))
self.area.addDock(
self.d1, 'left'
) ## place d1 at left edge of dock area (it will fill the whole space since there are no other docks yet)
self.area.addDock(self.d2, 'right',
self.d1) ## place d3 at bottom edge of d1
self.area.addDock(self.d4, 'bottom',
self.d2) ## place d4 at right edge of dock area
self.area.addDock(self.d3, 'bottom',
self.d4) ## place d5 at left edge of d1
# #old version
# self.imv = pg.ImageView()
# self.imv.setColorMap(pg.ColorMap(np.array([ 0. , 0.25, 0.5 , 0.75, 1. ]), np.array([[ 255, 255, 255, 255], [ 0, 0, 255, 255], [ 0, 0, 0, 255], [255, 0, 0, 255], [255, 255, 0, 255]], dtype=np.uint8)))
# self.imv.setImage(imread(r"D:\!Data\2016_04_22\01 T no_ramp a=-6 f=363.9 b=0.8\0ms\1_1.png"))
#
# self.imv.getHistogramWidget().setHistogramRange(0,0.6)
# self.imv.getHistogramWidget().setLevels(0, 0.6)
# self.d1.addWidget
# new version with ROI
win = pg.GraphicsLayoutWidget()
p1 = win.addPlot()
self.img = pg.ImageItem()
self.img.setZValue(1)
p1.addItem(self.img)
self.globals['image'] = imread(
r"D:\!Data\2016_04_22\01 T no_ramp a=-6 f=363.9 b=0.8\0ms\1_1.png")
self.img.setImage(self.globals['image'])
self.roi = pg.ROI(self.roi_center,
self.roi_size,
pen=pg.mkPen('g',
width=1)) #, style=pg.QtCore.Qt.DotLine
self.roi.addScaleHandle([1, 1], [0, 0])
# self.roi.addScaleHandle([1, 0.5], [0, 1])
p1.addItem(self.roi)
self.roi.setZValue(100)
self.hist = pg.HistogramLUTItem()
self.hist.setImageItem(self.img)
self.hist.setHistogramRange(0, 0.6)
self.hist.setLevels(0, 0.6)
self.hist.gradient.setColorMap(
pg.ColorMap(
np.array([0., 0.25, 0.5, 0.75, 1.]),
np.array(
[[255, 255, 255, 255], [0, 0, 255, 255], [0, 0, 0, 255],
[255, 0, 0, 255], [255, 255, 0, 255]],
dtype=np.uint8)))
win.addItem(self.hist)
# self.hist.sigLookupTableChanged.connect(self.LUTChanged)
self.img.setLookupTable(self.hist.getLookupTable(n=256))
self.roi.sigRegionChangeFinished.connect(self.updateROI)
self.d1.addWidget(win, col=0, row=0)
win2 = pg.GraphicsLayoutWidget()
p1_2 = win2.addPlot()
self.img2 = pg.ImageItem()
self.img2.setZValue(1)
# self.img2.setPxMode(True)
p1_2.addItem(self.img2)
self.globals['image2'] = imread(
r"D:\!Data\2016_04_22\01 T no_ramp a=-6 f=363.9 b=0.8\0ms\1_1.png")
self.img2.setImage(self.globals['image2'])
self.roi2 = pg.ROI(self.roi_center,
self.roi_size,
pen=pg.mkPen(
'g', width=1)) # , style=pg.QtCore.Qt.DotLine
self.roi2.addScaleHandle([1, 1], [0, 0])
# self.roi.addScaleHandle([1, 0.5], [0, 1])
p1_2.addItem(self.roi2)
self.roi2.setZValue(100)
self.hist2 = pg.HistogramLUTItem()
self.hist2.setImageItem(self.img2)
self.hist2.setHistogramRange(0, 0.6)
self.hist2.setLevels(0, 0.6)
self.hist2.gradient.setColorMap(
pg.ColorMap(
np.array([0., 0.25, 0.5, 0.75, 1.]),
np.array(
[[255, 255, 255, 255], [0, 0, 255, 255], [0, 0, 0, 255],
[255, 0, 0, 255], [255, 255, 0, 255]],
dtype=np.uint8)))
win2.addItem(self.hist2)
# self.hist.sigLookupTableChanged.connect(self.LUTChanged)
self.img2.setLookupTable(self.hist2.getLookupTable(n=256))
self.roi2.sigRegionChangeFinished.connect(self.updateROI2)
self.d1.addWidget(win2, col=0, row=1)
self.w2 = pg.PlotWidget()
self.w2.addLegend()
# self.w2.setYRange(0,100)
self.curve11 = self.w2.plot(np.array([]), pen=(255, 0, 0), name='Nx')
self.curve12 = self.w2.plot(np.array([]), pen=(0, 255, 0), name='Ny')
self.curve13 = self.w2.plot(np.array([]), pen=(0, 0, 255), name='N')
self.d2.addWidget(self.w2)
self.w3 = pg.TableWidget()
self.w3.setFont(QFont('Arial', 20))
self.w3.setData(self.image_data_to_display)
self.d3.addWidget(self.w3)
# w6 = QHBoxLayout()
# w6.addWidget(QLabel('fit1D_x'))
chbx_widget = QWidget()
chbx_layout = QHBoxLayout()
chbx_layout.addWidget(QLabel('fit1D_x'))
self.fit1D_x_chbx = QCheckBox()
self.fit1D_x_chbx.setChecked(self.do_fit1D_x)
self.fit1D_x_chbx.stateChanged.connect(
lambda state: self.chbxClicked('do_fit1D_x', state))
chbx_layout.addWidget(self.fit1D_x_chbx)
chbx_layout.addWidget(QLabel('fit1D_y'))
self.fit1D_y_chbx = QCheckBox()
self.fit1D_y_chbx.setChecked(self.do_fit1D_y)
self.fit1D_y_chbx.stateChanged.connect(
lambda state: self.chbxClicked('do_fit1D_y', state))
chbx_layout.addWidget(self.fit1D_y_chbx)
chbx_layout.addWidget(QLabel('fit2D'))
self.fit2D_chbx = QCheckBox()
self.fit2D_chbx.setChecked(self.do_fit2D)
self.fit2D_chbx.stateChanged.connect(
lambda state: self.chbxClicked('do_fit2D', state))
chbx_layout.addWidget(self.fit2D_chbx)
chbx_layout.addWidget(QLabel('substract background'))
self.fit2D_chbx = QCheckBox()
self.fit2D_chbx.setChecked(self.subs_bgnd)
self.fit2D_chbx.stateChanged.connect(
lambda state: self.chbxClicked('subs_bgnd', state))
chbx_layout.addWidget(self.fit2D_chbx)
chbx_layout.addWidget(QLabel('N points to show'))
self.n_points_spin_box = QSpinBox()
self.n_points_spin_box.setRange(10, 1000)
self.n_points_spin_box.setValue(self.N_point_to_plot)
self.n_points_spin_box.valueChanged.connect(self.nPointsChanged)
chbx_layout.addWidget(self.n_points_spin_box)
# w6.addWidget(self.fit1D_x_chbx)
# self.d3.addWidget(QLabel('fit1D_x'),row=1,col=0)
# self.d3.addWidget(self.fit1D_x_chbx,row=1,col=1)
chbx_layout.addStretch(1)
chbx_widget.setLayout(chbx_layout)
self.d3.addWidget(chbx_widget)
self.w5 = pg.TableWidget(editable=True, sortable=False)
self.w5.setFont(QFont('Arial', 20))
self.w5.setData(self.getROITableData())
self.w5.cellChanged.connect(self.roiTableChanged)
self.d3.addWidget(self.w5, row=0, col=1)
self.w4 = pg.PlotWidget()
# self.w2.setYRange(0,100)
self.w4.addLegend(size=(5, 20))
self.curve21 = self.w4.plot(np.array([]), pen=(255, 0, 0), name="w_x1")
self.curve22 = self.w4.plot(np.array([]), pen=(0, 255, 0), name="w_x2")
self.curve23 = self.w4.plot(np.array([]), pen=(0, 0, 255), name="w_y1")
self.curve24 = self.w4.plot(np.array([]), pen='y', name="w_y2")
self.d4.addWidget(self.w4)
self.signals.newImageRead.connect(self.routine)
def __init__(self, parent=None):
super(DetailThirdrowdata, self).__init__(parent)
self.layout = QGridLayout(self)
self.table = pg.TableWidget()
self.table.horizontalHeader().setHidden(True)
self.table.setShowGrid(False)
self.table.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
self.layout.addWidget(self.table)
self.thirdrowdata = [
(4, 56, 85, 5, 4, 56, 85, 5, " ", 4, 56, 85, 5, 4, 56, 85, 5, " ",
4, 56, 85, 5, 4, 56, 85, 5, " ", 4, 56, 85, 5, 4, 56, 85, 55),
(1, 20, 33, 8, 1, 20, 33, 8, " ", 1, 20, 33, 8, 1, 20, 33, 8, " ",
1, 20, 33, 8, 1, 20, 33, 8, " ", 1, 20, 33, 8, 1, 20, 33, 8),
(45, 4, 56, 85, 45, 4, 56, 85, " ", 45, 4, 56, 85, 45, 4, 56, 85,
" ", 45, 4, 56, 85, 45, 4, 56, 85, " ", 45, 4, 56, 85, 45, 4, 56,
85),
(1, 20, 33, 85, 1, 20, 33, 85, " ", 1, 20, 33, 85, 1, 20, 33, 85,
" ", 1, 20, 33, 85, 1, 20, 33, 85, " ", 1, 20, 33, 85, 1, 20, 33,
85),
(4, 56, 85, 6, 4, 56, 85, 6, " ", 4, 56, 85, 6, 4, 56, 85, 6, " ",
4, 56, 85, 6, 4, 56, 85, 6, " ", 4, 56, 85, 6, 4, 56, 85, 6),
(1, 2, 12, 33, 1, 2, 12, 33, " ", 1, 2, 12, 33, 1, 2, 12, 33, " ",
1, 2, 12, 33, 1, 2, 12, 33, " ", 1, 2, 12, 33, 1, 2, 12, 33)
]
self.showthirdrowdata = np.array(self.thirdrowdata,
dtype=[('No', int), ('Time', object),
('Source', object),
('Destination', object),
('object1', object),
('object2', object),
('object3', object),
('object4', object),
('object5', object),
('object6', object),
('object7', object),
('object8', object),
('object9', object),
('object10', object),
('object11', object),
('object12', object),
('object13', object),
('object14', object),
('object15', object),
('object16', object),
('object17', object),
('object18', object),
('object19', object),
('object20', object),
('object21', object),
('object22', object),
('object23', object),
('object24', object),
('object25', object),
('object26', object),
('object27', object),
('object28', object),
('object29', object),
('object30', object),
('object31', object)])
self.table.verticalHeader().setDefaultSectionSize(20)
self.table.setData(self.thirdrowdata)
self.setLayout(self.layout)
def __init__(self,
parent=None,
config_file='cam_config.json',
image_name='image',
default_image=r"default_camera.tiff",
image_stack_name='image_stack'):
self.config_file = config_file # where to save config
self.image_name = image_name # name of the image in parent.globals
self.image_stack_name = image_stack_name # name of image stack in parent globals (array of filenames to save)
self.parent = parent
self.config = {}
super().__init__()
# default. All theese will be downloaded from config file
self.do_fit1D_x = True
self.do_fit1D_y = True
self.do_fit2D = False
self.subs_bgnd = True
self.nAtoms = impr.N_atoms(gain=324,
exposure=909,
power=2.42,
width=2.43,
delta=7e6)
self.realSize = impr.real_size
self.n_sigmas = 3
self.roi_center = [200, 200]
self.roi_size = [100, 100]
# image data to show in table
self.image_data_to_display = np.array([('N0', 0, 0), ("X0", 0, 0),
('N', 0, 0), ('W', 0, 0),
('n,T', 0, 0)],
dtype=[(' ', object),
('x', object),
('y', object)])
self.load() # config loading
main_layout = QHBoxLayout()
self.win = pg.GraphicsLayoutWidget()
p1 = self.win.addPlot()
self.img = pg.ImageItem()
self.img.setZValue(1)
p1.addItem(self.img)
self.parent.globals[self.image_name] = imread(
default_image).T #initialise picture
self.img.setImage(self.parent.globals[self.image_name])
self.roi = pg.ROI(self.roi_center,
self.roi_size,
pen=pg.mkPen(
'g', width=1)) # , style=pg.QtCore.Qt.DotLine
self.roi.addScaleHandle([1, 1], [0, 0])
# self.roi.addScaleHandle([1, 0.5], [0, 1])
p1.addItem(self.roi)
self.roi.setZValue(100)
self.hist = pg.HistogramLUTItem()
self.hist.setImageItem(self.img)
self.hist.setHistogramRange(0, 0.6)
self.hist.setLevels(0, 0.6)
self.hist.gradient.setColorMap(
pg.ColorMap(
np.array([0., 0.25, 0.5, 0.75, 1.]),
np.array(
[[255, 255, 255, 255], [0, 0, 255, 255], [0, 0, 0, 255],
[255, 0, 0, 255], [255, 255, 0, 255]],
dtype=np.uint8)))
self.win.addItem(self.hist)
self.img.setLookupTable(self.hist.getLookupTable(n=256))
self.roi.sigRegionChangeFinished.connect(self.updateROI)
main_layout.addWidget(self.win)
chbx_layout = QVBoxLayout() # basically config and info layout
chbx_layout.addWidget(QLabel('fit1D_x'))
self.fit1D_x_chbx = QCheckBox()
self.fit1D_x_chbx.setChecked(self.do_fit1D_x)
self.fit1D_x_chbx.stateChanged.connect(
lambda state: self.chbxClicked('do_fit1D_x', state))
chbx_layout.addWidget(self.fit1D_x_chbx)
chbx_layout.addWidget(QLabel('fit1D_y'))
self.fit1D_y_chbx = QCheckBox()
self.fit1D_y_chbx.setChecked(self.do_fit1D_y)
self.fit1D_y_chbx.stateChanged.connect(
lambda state: self.chbxClicked('do_fit1D_y', state))
chbx_layout.addWidget(self.fit1D_y_chbx)
chbx_layout.addWidget(QLabel('fit2D'))
self.fit2D_chbx = QCheckBox()
self.fit2D_chbx.setChecked(self.do_fit2D)
self.fit2D_chbx.stateChanged.connect(
lambda state: self.chbxClicked('do_fit2D', state))
chbx_layout.addWidget(self.fit2D_chbx)
chbx_layout.addWidget(QLabel('substract background'))
self.fit2D_chbx = QCheckBox()
self.fit2D_chbx.setChecked(self.subs_bgnd)
self.fit2D_chbx.stateChanged.connect(
lambda state: self.chbxClicked('subs_bgnd', state))
chbx_layout.addWidget(self.fit2D_chbx)
self.w3 = pg.TableWidget()
self.w3.setFixedWidth(160)
self.w3.setFont(QFont('Arial', 12))
self.w3.setData(self.image_data_to_display)
chbx_layout.addWidget(self.w3)
self.w3.horizontalHeader().setDefaultSectionSize(40)
self.w3.verticalHeader().setDefaultSectionSize(30)
self.w3.horizontalHeader().setResizeMode(QHeaderView.Fixed)
self.w3.verticalHeader().setResizeMode(QHeaderView.Fixed)
self.exp = QLineEdit('909')
self.exp.setFixedWidth(60)
chbx_layout.addWidget(self.exp)
self.exp.textChanged.connect(self.newCameraSettings)
self.gain = QLineEdit('324')
self.gain.setFixedWidth(60)
chbx_layout.addWidget(self.gain)
self.gain.textChanged.connect(self.newCameraSettings)
self.binn = QLineEdit('2')
self.binn.setFixedWidth(60)
chbx_layout.addWidget(self.binn)
self.binn.textChanged.connect(self.newCameraSettings)
self.power = QLineEdit('2.55')
self.power.setFixedWidth(60)
chbx_layout.addWidget(self.power)
self.power.textChanged.connect(self.newCameraSettings)
self.delta = QLineEdit('7.0')
self.delta.setFixedWidth(60)
chbx_layout.addWidget(self.delta)
self.delta.textChanged.connect(self.newCameraSettings)
chbx_layout.addStretch(1)
main_layout.addLayout(chbx_layout)
self.setLayout(main_layout)
