def initUI(self):
""""Assembles the basic Gui layout, status bar, menubar
toolbar etc."""
# status bar
self.statusBar().showMessage('Ready')
# actions
soundAction = QtGui.QAction(QtGui.QIcon.fromTheme('media-playback-start'),
'Play Sound', self)
soundAction.setShortcut('Ctrl+S')
soundAction.setStatusTip('Play data as sound')
soundAction.triggered.connect(self.playSound)
exitAction = QtGui.\
QAction(QtGui.QIcon.fromTheme('window-close'),
'Exit', self)
exitAction.setShortcut('Ctrl+Q')
exitAction.setStatusTip('Exit application')
exitAction.triggered.connect(QtGui.qApp.quit)
openAction = QtGui.\
QAction(QtGui.QIcon.fromTheme('document-open'), 'Open', self)
openAction.setShortcut('Ctrl+O')
openAction.setStatusTip('Open an arf file')
openAction.triggered.connect(self.showDialog)
exportAction = QtGui.QAction(QtGui.QIcon.fromTheme('document-save-as'),
'Export checked', self)
exportAction.setShortcut('Ctrl+e')
exportAction.setStatusTip('Export dataset as wav')
exportAction.triggered.connect(self.export)
plotcheckedAction = QtGui.QAction(QtGui.QIcon.fromTheme('face-smile'),
'Plot checked', self)
plotcheckedAction.setShortcut('Ctrl+k')
plotcheckedAction.setStatusTip('plot checked')
plotcheckedAction.triggered.connect(self.toggleplotchecked)
self.plotcheckedAction = plotcheckedAction
refreshAction = QtGui.QAction(QtGui.QIcon.fromTheme('view-refresh'),
'Refresh Data View', self)
refreshAction.setShortcut('Ctrl+r')
refreshAction.setStatusTip('Refresh Data View')
refreshAction.triggered.connect(self.refresh_data_view)
labelAction = QtGui.QAction(QtGui.QIcon.fromTheme('insert-object'),
'Add Label', self)
labelAction.setVisible(False)
labelAction.setShortcut('Ctrl+l')
labelAction.setStatusTip('Add label entry to current group')
labelAction.triggered.connect(self.add_label)
self.labelAction = labelAction
addPlotAction = QtGui.QAction('Add Plot', self)
addPlotAction.setVisible(False)
addPlotAction.setStatusTip('Add checked datasets to current plot')
addPlotAction.triggered.connect(self.add_plot)
self.addPlotAction = addPlotAction
# menubar
menubar = self.menuBar()
fileMenu = menubar.addMenu('&File')
fileMenu.addAction(exitAction)
fileMenu.addAction(openAction)
fileMenu.addAction(exportAction)
fileMenu.addAction(plotcheckedAction)
fileMenu.addAction(refreshAction)
# toolbar
self.toolbar = self.addToolBar('Toolbar')
self.toolbar.addAction(exitAction)
self.toolbar.addAction(openAction)
self.toolbar.addAction(soundAction)
self.toolbar.addAction(exportAction)
self.toolbar.addAction(plotcheckedAction)
self.toolbar.addAction(refreshAction)
self.toolbar.addAction(labelAction)
self.toolbar.addAction(addPlotAction)
# file tree
self.tree_view = DataTreeView()
self.tree_view.currentItemChanged.connect(self.selectEntry)
if self.current_file:
self.populateTree()
# tree_toolbar
self.tree_toolbar = treeToolBar(self.tree_view)
#attribute table
self.attr_table = QtGui.QTableWidget(10, 2)
self.attr_table.setHorizontalHeaderLabels(('key','value'))
#plot region
self.data_layout = pg.GraphicsLayoutWidget()
self.subplots=[]
#settings panel
self.settings_panel = settingsPanel()
# final steps
self.area = pgd.DockArea()
tree_dock = pgd.Dock("Tree", size=(200, 100))
data_dock = pgd.Dock("Data", size=(500, 200))
attr_table_dock = pgd.Dock("Attributes", size=(200, 50))
settings_dock = pgd.Dock('Settings', size=(150,1))
self.area.addDock(tree_dock, 'left')
self.area.addDock(data_dock, 'right')
self.area.addDock(attr_table_dock, 'bottom', tree_dock)
self.area.addDock(settings_dock, 'bottom', attr_table_dock)
tree_dock.addWidget(self.tree_view)
tree_dock.addWidget(self.tree_toolbar)
tree_dock.addAction(exitAction)
data_dock.addWidget(self.data_layout)
attr_table_dock.addWidget(self.attr_table)
settings_dock.addWidget(self.settings_panel)
self.settings_panel.show()
self.setCentralWidget(self.area)
self.setWindowTitle('arfview')
self.resize(1300, 700)
self.show()
class MainWindow(QtGui.QMainWindow):
'''the main window of the program'''
def __init__(self):
super(MainWindow, self).__init__()
self.current_file = None
self.open_files = [] # TODO replace current_file with list
self.plotchecked = False
self.initUI()
def initUI(self):
""""Assembles the basic Gui layout, status bar, menubar
toolbar etc."""
# status bar
self.statusBar().showMessage('Ready')
# actions
soundAction = QtGui.QAction(QtGui.QIcon.fromTheme('media-playback-start'),
'Play Sound', self)
soundAction.setShortcut('Ctrl+S')
soundAction.setStatusTip('Play data as sound')
soundAction.triggered.connect(self.playSound)
exitAction = QtGui.\
QAction(QtGui.QIcon.fromTheme('window-close'),
'Exit', self)
exitAction.setShortcut('Ctrl+Q')
exitAction.setStatusTip('Exit application')
exitAction.triggered.connect(QtGui.qApp.quit)
openAction = QtGui.\
QAction(QtGui.QIcon.fromTheme('document-open'), 'Open', self)
openAction.setShortcut('Ctrl+O')
openAction.setStatusTip('Open an arf file')
openAction.triggered.connect(self.showDialog)
exportAction = QtGui.QAction(QtGui.QIcon.fromTheme('document-save-as'),
'Export checked', self)
exportAction.setShortcut('Ctrl+e')
exportAction.setStatusTip('Export dataset as wav')
exportAction.triggered.connect(self.export)
plotcheckedAction = QtGui.QAction(QtGui.QIcon.fromTheme('face-smile'),
'Plot checked', self)
plotcheckedAction.setShortcut('Ctrl+k')
plotcheckedAction.setStatusTip('plot checked')
plotcheckedAction.triggered.connect(self.toggleplotchecked)
self.plotcheckedAction = plotcheckedAction
refreshAction = QtGui.QAction(QtGui.QIcon.fromTheme('view-refresh'),
'Refresh Data View', self)
refreshAction.setShortcut('Ctrl+r')
refreshAction.setStatusTip('Refresh Data View')
refreshAction.triggered.connect(self.refresh_data_view)
labelAction = QtGui.QAction(QtGui.QIcon.fromTheme('insert-object'),
'Add Label', self)
labelAction.setVisible(False)
labelAction.setShortcut('Ctrl+l')
labelAction.setStatusTip('Add label entry to current group')
labelAction.triggered.connect(self.add_label)
self.labelAction = labelAction
addPlotAction = QtGui.QAction('Add Plot', self)
addPlotAction.setVisible(False)
addPlotAction.setStatusTip('Add checked datasets to current plot')
addPlotAction.triggered.connect(self.add_plot)
self.addPlotAction = addPlotAction
# menubar
menubar = self.menuBar()
fileMenu = menubar.addMenu('&File')
fileMenu.addAction(exitAction)
fileMenu.addAction(openAction)
fileMenu.addAction(exportAction)
fileMenu.addAction(plotcheckedAction)
fileMenu.addAction(refreshAction)
# toolbar
self.toolbar = self.addToolBar('Toolbar')
self.toolbar.addAction(exitAction)
self.toolbar.addAction(openAction)
self.toolbar.addAction(soundAction)
self.toolbar.addAction(exportAction)
self.toolbar.addAction(plotcheckedAction)
self.toolbar.addAction(refreshAction)
self.toolbar.addAction(labelAction)
self.toolbar.addAction(addPlotAction)
# file tree
self.tree_view = DataTreeView()
self.tree_view.currentItemChanged.connect(self.selectEntry)
if self.current_file:
self.populateTree()
# tree_toolbar
self.tree_toolbar = treeToolBar(self.tree_view)
#attribute table
self.attr_table = QtGui.QTableWidget(10, 2)
self.attr_table.setHorizontalHeaderLabels(('key','value'))
#plot region
self.data_layout = pg.GraphicsLayoutWidget()
self.subplots=[]
#settings panel
self.settings_panel = settingsPanel()
# final steps
self.area = pgd.DockArea()
tree_dock = pgd.Dock("Tree", size=(200, 100))
data_dock = pgd.Dock("Data", size=(500, 200))
attr_table_dock = pgd.Dock("Attributes", size=(200, 50))
settings_dock = pgd.Dock('Settings', size=(150,1))
self.area.addDock(tree_dock, 'left')
self.area.addDock(data_dock, 'right')
self.area.addDock(attr_table_dock, 'bottom', tree_dock)
self.area.addDock(settings_dock, 'bottom', attr_table_dock)
tree_dock.addWidget(self.tree_view)
tree_dock.addWidget(self.tree_toolbar)
tree_dock.addAction(exitAction)
data_dock.addWidget(self.data_layout)
attr_table_dock.addWidget(self.attr_table)
settings_dock.addWidget(self.settings_panel)
self.settings_panel.show()
self.setCentralWidget(self.area)
self.setWindowTitle('arfview')
self.resize(1300, 700)
self.show()
def toggleplotchecked(self):
self.plotchecked = not self.plotchecked
print('plot checked: ' + str(self.plotchecked))
if self.plotchecked:
self.plotcheckedAction.setIcon(QtGui.QIcon.fromTheme('face-cool'))
self.plotcheckedAction.setStatusTip('click to turn check mode off')
self.plotcheckedAction.setText('check mode is on')
self.plotcheckedAction.setIconText('check mode is on')
self.addPlotAction.setVisible(True)
else:
self.plotcheckedAction.setIcon(QtGui.QIcon.fromTheme('face-smile'))
self.plotcheckedAction.setStatusTip('click to turn check mode on')
self.plotcheckedAction.setText('check mode is off')
self.plotcheckedAction.setIconText('check mode is off')
self.addPlotAction.setVisible(False)
def export(self):
items = self.tree_view.all_checked_dataset_elements()
if not items: return
savedir, filename = os.path.split(items[0].file.filename)
savepath = os.path.join(savedir,os.path.splitext(filename)[0]
+ '_' + items[0].name.replace('/','_'))
print(savepath)
fname, fileextension = QtGui.QFileDialog.\
getSaveFileName(self, 'Save data as',
savepath,
'wav (*.wav);;text (*.csv, *.dat)')
for i,item in enumerate(items):
if 'datatype' in item.attrs.keys() and item.attrs['datatype'] < 1000:
if i:
fname = os.path.join(savedir,os.path.splitext(filename)[0]
+ '_' + item.name.replace('/','_'))
export(item, fileextension.split(' ')[0], fname)
def playSound(self):
item = self.tree_view.currentItem().getData()
playSound(item, self)
def showDialog(self):
extensions = '*.arf *.hdf5 *.h5 *.mat *.wav *.lbl'
#added because not all of arfx compiles on OS X
try:
from arfx import pcmio
extensions += ' *.pcm'
except ImportError:
pass
fname, fileextension = QtGui.QFileDialog.\
getOpenFileName(self, 'Open file', '.', extensions)
if not fname: return
print(fileextension)
ext = os.path.splitext(fname)[-1]
if ext not in ('.arf','.hdf5','.h5','.mat'):
if ext in ('.lbl', '.wav'):
temp_h5f = createtemparf(fname)
elif ext in ('.pcm', '.pcm_seq2'):
# reversing value and key to access type number from datatype_name
sampled_types = {value:key for key,value in named_types.items()
if key > 0 and key < 1000}
datatype_name,ok = QtGui.QInputDialog.getItem(self, "",
"Select datatype of file",
sampled_types.keys())
if not ok: return
temp_h5f = createtemparf(fname, datatype=sampled_types[datatype_name])
fname = temp_h5f.file.filename
print("%s opened" % (fname))
self.statusBar().showMessage("%s opened" % (fname))
self.current_file = h5py.File(str(fname))
self.populateTree()
# selects first entry if first file opened
item=self.tree_view.topLevelItem(0)
if item.getData().file.filename == fname:
#self.selectEntry(item.child(0))
self.tree_view.setCurrentItem(item.child(0))
def populateTree(self):
f = self.current_file
root = f['/']
self.tree_view.recursivePopulateTree(root)
def refresh_data_view(self):
checked_datasets = self.tree_view.all_checked_dataset_elements()
if len(checked_datasets) > 0 and self.plotchecked:
self.plot_dataset_list(checked_datasets, self.data_layout)
else:
item = self.tree_view.currentItem().getData()
if type(item) == h5py.Dataset:
datasets = [item]
else:
datasets = [x for x in item.values() if type(x) == h5py.Dataset]
self.plot_dataset_list(datasets, self.data_layout)
def add_plot(self):
checked_datasets = self.tree_view.all_checked_dataset_elements()
if len(checked_datasets) > 0 and self.plotchecked:
new_layout = self.data_layout.addLayout(row=len(self.subplots),col=0)
self.plot_dataset_list(checked_datasets, new_layout)
def selectEntry(self, treeItem):
item = treeItem.getData()
populateAttrTable(self.attr_table, item)
if not self.plotchecked:
self.refresh_data_view()
if (isinstance(item, h5py.Dataset) or isinstance(item, h5py.Group)
and item.name != '/'):
self.labelAction.setVisible(True)
else:
self.labelAction.setVisible(False)
def add_label(self):
item = self.tree_view.currentItem()
if isinstance(item.getData(), h5py.Group):
lbl_parent = item
elif isinstance(item.getData(), h5py.Dataset):
lbl_parent = item.parent()
lbl_rec = np.zeros((0,),dtype=[('name', 'a8'), ('start',float), ('stop', float)])
dset_name = 'lbl'
#naming new label dataset if 'lbl' is already in group
idx = 1
while dset_name in lbl_parent.getData().keys():
dset_name = 'lbl_%d' %(idx)
idx += 1
dset = lbl_parent.getData().create_dataset(dset_name,
data=lbl_rec,
maxshape=(None,))
dset.attrs.create('units','ms')
dset.attrs.create('datatype',2002)
self.tree_view.add(dset, parent_node=lbl_parent)
self.refresh_data_view()
def plot_dataset_list(self, dataset_list, data_layout, append=False):
''' plots a list of datasets to a data layout'''
data_layout.clear()
if not append:
self.subplots = []
# rasterQPainterPath = QtGui.QPainterPath().addRect(-.1,-5,.2,1) # TODO make a better raster
# shape that works
toes = []
for dataset in dataset_list:
print(dataset)
if 'datatype' not in dataset.attrs.keys():
print('{} is not an arf dataset'.format(repr(dataset)))
if os.path.basename(dataset.name) == 'jill_log':
print(dataset.value)
continue
'''sampled data'''
if dataset.attrs['datatype'] < 1000: # sampled data
if (self.settings_panel.oscillogram_check.checkState()
==QtCore.Qt.Checked):
pl = downsamplePlot(dataset, title=dataset.name,
name=str(len(self.subplots)))
data_layout.addItem(pl,row=len(self.subplots), col=0)
pl.setXRange(0, dataset.size/float(dataset.attrs['sampling_rate']))
pl.setYRange(np.min(dataset), np.max(dataset))
self.subplots.append(pl)
pl.showGrid(x=True, y=True)
''' simple events '''
elif utils.is_simple_event(dataset):
if dataset.attrs['units'] == 'ms':
data = dataset.value / 1000.
elif dataset.attrs['units'] == 'samples':
data = dataset.value / dataset.attrs['sampling_rate']
else:
data = dataset.value
if (self.settings_panel.raster_check.checkState()==QtCore.Qt.Checked or
self.settings_panel.psth_check.checkState()==QtCore.Qt.Checked or
self.settings_panel.isi_check.checkState()==QtCore.Qt.Checked):
toes.append(data)
continue
''' complex event '''
elif utils.is_complex_event(dataset):
if (self.settings_panel.label_check.checkState()
==QtCore.Qt.Checked):
#creating new extensible dataset if not extensible
if dataset.maxshape != (None,):
data = dataset[:]
name = dataset.name
group= dataset.parent
attributes = dataset.attrs
del group[name]
del dataset
dataset = arf.create_dataset(group, name, data,
maxshape=(None,),**attributes)
pl = labelPlot(dataset, title=dataset.name, name=str(len(self.subplots)))
data_layout.addItem(pl, row=len(self.subplots), col=0)
pl.showLabel('left', show=False)
self.subplots.append(pl)
else:
print('I don\'t know how to plot {} of type {} \
with datatype {}'.format(dataset,
type(dataset),
dataset.attrs['datatype']))
continue
'''adding spectrograms'''
if dataset.attrs['datatype'] in [0, 1]: # show spectrogram
if (self.settings_panel.spectrogram_check.checkState()
==QtCore.Qt.Checked):
#getting spectrogram settings
sr = float(dataset.attrs['sampling_rate'])
win_size_text = self.settings_panel.win_size.text()
t_step_text = self.settings_panel.step.text()
min_text = self.settings_panel.freq_min.text()
max_text = self.settings_panel.freq_max.text()
if win_size_text:
win_size = int(float(win_size_text))
else:
win_size = self.settings_panel.defaults['win_size']
self.settings_panel.win_size.setText(str(win_size))
if t_step_text:
t_step = int(float(t_step_text) * sr/1000.)
else:
t_step = self.settings_panel.defaults['step']
self.settings_panel.win_size.setText(str(int(tstep*1000)))
if min_text:
freq_min = int(min_text)
else:
freq_min = self.settings_panel.defaults['freq_min']
self.settings_panel.freq_min.setText(str(freq_min))
if max_text:
freq_max = int(max_text)
else:
freq_max = self.settings_panel.defaults['freq_max']
self.settings_panel.freq_max.setText(str(freq_max))
window_name = self.settings_panel.window.currentText()
if window_name == "Hann":
window = scipy.signal.hann(win_size)
elif window_name == "Bartlett":
window = scipy.signal.bartlett(win_size)
elif window_name == "Blackman":
window = scipy.signal.blackman(win_size)
elif window_name == "Boxcar":
window = scipy.signal.boxcar(win_size)
elif window_name == "Hamming":
window = scipy.signal.hamming(win_size)
elif window_name == "Parzen":
window = scipy.signal.parzen(win_size)
#computing and interpolating image
Pxx = libtfr.stft(dataset,w=window,step=t_step)
spec = np.log(Pxx.T)
res_factor = 1.0 #factor by which resolution is increased
# spec = interpolate_spectrogram(spec, res_factor=res_factor)
#making color lookup table
pos = np.linspace(0,1,7)
color = np.array([[100,100,255,255],[0,0,255,255],[0,255,255,255],[0,255,0,255],
[255,255,0,255],[255,0,0,255],[100,0,0,255]], dtype=np.ubyte)
color_map = pg.ColorMap(pos,color)
lut = color_map.getLookupTable(0.0,1.0,256)
img = pg.ImageItem(spec,lut=lut)
#img.setLevels((-5, 10))
pl = data_layout.addPlot(name=str(len(self.subplots)), row=len(self.subplots), col=0)
self.subplots.append(pl)
pl.addItem(img)
image_scale = t_step/sr/res_factor
img.setScale(image_scale)
df = sr/float(win_size)
plot_scale = df/res_factor/image_scale
pl.getAxis('left').setScale(plot_scale)
pl.setXRange(0, dataset.size / dataset.attrs['sampling_rate'])
pl.setYRange(freq_min/plot_scale, freq_max/plot_scale)
pl.setMouseEnabled(x=True, y=False)
if toes:
if self.settings_panel.raster_check.checkState()==QtCore.Qt.Checked:
pl= rasterPlot(toes)
data_layout.addItem(pl, row=len(self.subplots), col=0)
pl.showLabel('left', show=False)
self.subplots.append(pl)
if self.settings_panel.psth_check.checkState()==QtCore.Qt.Checked:
all_toes = np.zeros(sum(len(t) for t in toes))
k=0
for t in toes:
all_toes[k:k+len(t)] = t
k += len(t)
if self.settings_panel.psth_bin_size.text():
bin_size = float(self.settings_panel.psth_bin_size.text())/1000.
else:
bin_size = .01
bins = np.arange(all_toes.min(),all_toes.max()+bin_size,bin_size)
y,x = np.histogram(all_toes,bins=bins)
psth = pg.PlotCurveItem(x, y, stepMode=True,
fillLevel=0, brush=(0, 0, 255, 80))
pl = data_layout.addPlot(row=len(self.subplots), col=0)
pl.addItem(psth)
pl.setMouseEnabled(y=False)
self.subplots.append(pl)
if self.settings_panel.isi_check.checkState()==QtCore.Qt.Checked:
isis = np.zeros(sum(len(t)-1 for t in toes))
k=0
for t in toes:
isis[k:k+len(t)-1] = np.diff(t)
k += len(t)-1
if self.settings_panel.psth_bin_size.text():
bin_size = float(self.settings_panel.psth_bin_size.text())/1000.
else:
bin_size = .01
bins = np.arange(isis.min(),isis.max()+bin_size,bin_size)
y,x = np.histogram(isis,bins=bins,normed=True)
isi_hist = pg.PlotCurveItem(x, y, stepMode=True,
fillLevel=0, brush=(0, 0, 255, 80))
pl = data_layout.addPlot(row=len(self.subplots), col=0)
pl.addItem(isi_hist)
pl.setMouseEnabled(y=False)
self.subplots.append(pl)
'''linking x axes'''
masterXLink = None
for pl in self.subplots:
if not masterXLink:
masterXLink = pl
pl.setXLink(masterXLink)
