def restore_settings(self, do_restore, filename=None):
if (filename):
s = QtCore.QSettings(filename, QtCore.QSettings.IniFormat)
else:
s = QtCore.QSettings()
self._init_geometry(s)
self._init_recorder(s)
loaded_sources = []
try:
if do_restore:
loaded_sources = self._init_data_sources(s)
except (TypeError, KeyError):
# raise
#raise
# Be a bit more resilient against configuration problems
logging.warning(
"Failed to load data source settings! Continuing...")
if do_restore:
try:
self._restore_data_windows(s, loaded_sources)
except (TypeError, KeyError):
# Be a bit more resilient against configuration problems
logging.warning(
"Failed to load data windows settings! Continuing...")
self.plotdata_widget.restore_state(s)
self.settings = s
def __init__(self, parent=None):
QtGui.QMainWindow.__init__(self, None)
self.setAttribute(QtCore.Qt.WA_DeleteOnClose)
self._enabled_sources = {}
self.settings = QtCore.QSettings()
self.setupUi(self)
self.alertBlinkTimer = QtCore.QTimer()
self.alertBlinkTimer.setInterval(500)
self._setup_connections()
self._parent = parent
# If True this DataWindow was restored from saved settings
self.restored = False
self.alertBlinking = False
self.set_sounds_and_volume()
def save_settings(self, filename=None):
if (filename):
s = QtCore.QSettings(filename, QtCore.QSettings.IniFormat)
else:
s = QtCore.QSettings()
s.setValue("geometry", self.saveGeometry())
s.setValue("windowState", self.saveState())
# Save data sources
ds_settings = []
for ds in self._data_sources:
ds_settings.append([ds.hostname, ds.port, ds.ssh_tunnel, ds.conf])
s.setValue("dataSources", ds_settings)
self.plotdata_widget.save_state(s)
s.setValue("plotData", self.plotdata_widget.save_plotdata())
s.setValue("dataWindows", self.save_data_windows())
# Make sure settings are saved
s.sync()
def _update_bg(self):
if self._settings_diag.bg is not None:
VB = self.plot.getViewBox()
B = pyqtgraph.ImageItem(image=self._settings_diag.bg, autoLevels=True)
xmin = float(self._settings_diag.bg_xmin.text())
ymin = float(self._settings_diag.bg_xmin.text())
width = float(self._settings_diag.bg_xmax.text()) - xmin
height = float(self._settings_diag.bg_ymax.text()) - ymin
rect = QtCore.QRectF(xmin, ymin, width, height)
B.setRect(rect)
VB.addItem(B, ignoreBounds=True)
def __init__(self, _type, parent=None, **kwargs):
QtCore.QObject.__init__(self, parent, **kwargs)
ctx = ZmqContext.instance()
self._socket = ctx.socket(_type)
fd = self._socket.getsockopt(FD)
self._notifier = QtCore.QSocketNotifier(fd, QtCore.QSocketNotifier.Read, self)
self._notifier.activated.connect(self.activity)
self._socket.setsockopt(RCVHWM, 100)
self.filters = []
def _init_timer(self):
"""Initialize reploting timer."""
self._replot_timer = QtCore.QTimer()
self._replot_timer.setInterval(1000) # Replot every 1000 ms
self._replot_timer.timeout.connect(self._replot)
self._replot_timer.start()
def __init__(self, parent):
QtGui.QDialog.__init__(self, parent, QtCore.Qt.WindowTitleHint)
self.setupUi(self)
settings = QtCore.QSettings()
self.outputPath.setText(settings.value("outputPath"))
class DataSource(QtCore.QObject):
"""Manages a connection with one backend"""
plotdata_added = QtCore.Signal(PlotData)
subscribed = QtCore.Signal(str)
unsubscribed = QtCore.Signal(str)
def __init__(self, parent, hostname, port, ssh_tunnel=None, conf={}):
QtCore.QObject.__init__(self, parent)
self._hostname = hostname
self._port = port
self._ssh_tunnel = ssh_tunnel
self.connected = False
self._plotdata = {}
self._subscribed_titles = {}
self._recorded_titles = {}
self._recorder = None
self._data_socket = ZmqSocket(SUB, self)
self.conf = conf
self._group_structure = {}
try:
self._connect()
self.connected = True
self._get_data_port()
self.titles = None
self.data_type = None
except (RuntimeError, zmq.error.ZMQError):
QtGui.QMessageBox.warning(self.parent(), "Connection failed!",
"Could not connect to %s" % self.name())
raise
def subscribe(self, title, plot):
"""Subscribe to the broadcast named title, and associate it with the given plot"""
if title not in self._subscribed_titles:
self._subscribed_titles[title] = [plot]
try:
self._data_socket.subscribe(title)
self.subscribed.emit(title)
logging.debug("Subscribing to %s on %s.", title, self.name())
# socket might still not exist
except AttributeError:
pass
else:
self._subscribed_titles[title].append(plot)
def unsubscribe(self, title, plot):
"""Dissociate the given plot with the broadcast named title.
If no one else is associated with it unsubscribe"""
self._subscribed_titles[title].remove(plot)
# Check if list is empty
if not self._subscribed_titles[title]:
self._data_socket.unsubscribe(title)
self.unsubscribed.emit(title)
logging.debug("Unsubscribing from %s on %s.", title, self.name())
self._subscribed_titles.pop(title)
def subscribe_for_recording(self, title):
"""Subscribe to the broadcast named title, and associate it with recorder"""
# Only subscribe if we are not already subscribing for plotting
if title in self._subscribed_titles:
return
if title not in self._recorded_titles:
self._recorded_titles[title] = True
try:
self._data_socket.subscribe(title)
self.subscribed.emit(title)
logging.debug("Subscribing to %s on %s.", title, self.name())
# socket might still not exist
except AttributeError:
pass
def unsubscribe_for_recording(self, title):
"""Dissociate the recorder with the broadcast named title.
If no one else is associated with it unsubscrine"""
self._recorded_titles[title] = False
if not title in self._subscribed_titles:
self._data_socket.unsubscribe(title)
self.unsubscribed.emit(title)
logging.debug("Unsubscribing from %s on %s.", title, self.name())
self._recorded_titles.pop(title)
def name(self):
"""Return a string representation of the data source"""
if (self._ssh_tunnel):
return '%s (%s)' % (self._hostname, self._ssh_tunnel)
else:
return self._hostname
@property
def plotdata(self):
"""Returns the data source dictionary of plotdata"""
return self._plotdata
def _connect(self):
"""Connect to the configured backend"""
self._ctrl_socket = ZmqSocket(REQ)
addr = "tcp://%s:%d" % (self._hostname, self._port)
self._ctrl_socket.ready_read.connect(self._get_request_reply)
self._ctrl_socket.connect_socket(addr, self._ssh_tunnel)
def _get_data_port(self):
"""Ask to the backend for the data port"""
self._ctrl_socket.send_multipart(['data_port'.encode('UTF-8')])
def query_configuration(self):
"""Ask to the backend for the configuration"""
self._ctrl_socket.send_multipart(['conf'.encode('UTF-8')])
def query_reloading(self):
"""Ask the backend to reload its configuration"""
self._ctrl_socket.send_multipart(['reload'.encode('UTF-8')])
def _get_request_reply(self, socket=None):
"""Handle the reply of the backend to a previous request"""
if (socket is None):
socket = self.sender()
reply = socket.recv_json()
if (reply[0] == 'data_port'):
self._data_port = reply[1]
logging.debug("Data source '%s' received data_port=%s",
self.name(), self._data_port)
addr = "tcp://%s:%s" % (self._hostname, self._data_port)
self._data_socket.ready_read.connect(self._get_broadcast)
self._data_socket.connect_socket(addr, self._ssh_tunnel)
self.parent().add_backend(self)
# Subscribe to stuff already requested
for title in self._subscribed_titles.keys():
self._data_socket.subscribe(title)
self.subscribed.emit(title)
logging.debug("Subscribing to %s on %s.", title, self.name())
self.query_configuration()
elif (reply[0] == 'conf'):
self.conf = reply[1]
self.titles = self.conf.keys()
self.data_type = {}
for k in self.conf.keys():
if ('data_type' not in self.conf[k]):
# Broadcasts without any data will not have a data_type
# Let's remove them from the title list and continue
self.titles.remove(k)
continue
self.data_type[k] = self.conf[k]['data_type']
if (k not in self._plotdata):
if "group" in self.conf[k]:
group = self.conf[k]["group"]
if group is None:
group = "No group"
else:
group = "No group"
self._plotdata[k] = PlotData(self, k, group=group)
self.plotdata_added.emit(self._plotdata[k])
self.add_item_to_group_structure(k, group)
# Remove PlotData which is no longer in the conf
for k in self._plotdata.keys():
if k not in self.titles:
self._plotdata.pop(k)
def _get_broadcast(self):
"""Receive a data package on the data socket"""
socket = self.sender()
socket.blockSignals(True)
QtCore.QCoreApplication.processEvents()
socket.blockSignals(False)
# Discard key
socket.recv()
data = socket.recv_json()
for i in range(len(data)):
if data[i] == '__ndarray__':
data[i] = socket.recv_array()
self._process_broadcast(data)
def _process_broadcast(self, payload):
"""Handle a data package received by the data socket"""
cmd = payload[1]
title = payload[2]
data = payload[3]
if (title not in self.conf):
# We're getting data we were not expecting
# Let's discard it and order an immediate reconfigure
logging.debug(
"Received unexpected data with title %s on %s. Reconfiguring...",
title, self.name())
return
if (cmd == 'new_data'):
data_x = payload[4]
# At the moment x is always a timestamp so I'll add some metadata to show it
if type(data_x) is not numpy.ndarray:
data_x = numpy.array(data_x)
data_x.dtype = numpy.dtype(data_x.dtype, metadata={'units': 's'})
conf = payload[5]
self.conf[title].update(conf)
if self._plotdata[title].recordhistory:
self._recorder.append(title, data, data_x)
if 'sum_over' in conf:
if 'msg' in conf:
self._plotdata[title].sum_over(data, data_x, conf['msg'])
else:
self._plotdata[title].sum_over(data, data_x, '')
else:
if 'msg' in conf:
self._plotdata[title].append(data, data_x, conf['msg'])
else:
self._plotdata[title].append(data, data_x, '')
@property
def hostname(self):
"""Give access to the data source hostname"""
return self._hostname
@property
def port(self):
"""Give access to the data source port"""
return self._port
@property
def ssh_tunnel(self):
"""Give access to the data source ssh_tunnel"""
return self._ssh_tunnel
@property
def subscribed_titles(self):
"""Returns the currently subscribed titles"""
return self._subscribed_titles.keys()
def restore_state(self, state):
"""Restores any plotdata that are saved in the state"""
for pds in state:
if (pds['data_source'][0] == self.hostname
and pds['data_source'][1] == self.port
and pds['data_source'][2] == self.ssh_tunnel):
# It's a match!
k = pds['title']
group = pds["group"]
pd = PlotData(self, k, group=group)
pd.restore_state(pds, self)
self._plotdata[k] = pd
self.plotdata_added.emit(self._plotdata[k])
self.add_item_to_group_structure(k, group)
@property
def group_structure(self):
return self._group_structure
def add_item_to_group_structure(self, title, group):
if group in self.group_structure:
self.group_structure[group].append(title)
else:
self.group_structure[group] = [title]
class ImageView(QtGui.QWidget):
"""
Widget used for display and analysis of image data.
Implements many features:
* Displays 2D and 3D image data. For 3D data, a z-axis
slider is displayed allowing the user to select which frame is displayed.
* Displays histogram of image data with movable region defining the dark/light levels
* Editable gradient provides a color lookup table
* Frame slider may also be moved using left/right arrow keys as well as pgup, pgdn, home, and end.
* Basic analysis features including:
* ROI and embedded plot for measuring image values across frames
* Image normalization / background subtraction
Basic Usage::
imv = pg.ImageView()
imv.show()
imv.setImage(data)
"""
sigProcessingChanged = QtCore.Signal(object)
def __init__(self, parent=None, name="ImageView", view=None, imageItem=None, *args):
"""
By default, this class creates an :class:`ImageItem <pyqtgraph.ImageItem>` to display image data
and a :class:`ViewBox <pyqtgraph.ViewBox>` to contain the ImageItem. Custom items may be given instead
by specifying the *view* and/or *imageItem* arguments.
"""
QtGui.QWidget.__init__(self, parent, *args)
self._parent = parent
self.levelMax = 4096
self.levelMin = 0
self.name = name
self.image = None
self.axes = {}
self.imageDisp = None
self.ui = Ui_Form()
self.ui.setupUi(self)
self.scene = self.ui.graphicsView.scene()
if view is None:
self.view = pyqtgraph.ViewBox()
else:
self.view = view
self.ui.graphicsView.setCentralItem(self.view)
self.view.setAspectLocked(True)
self.view.invertY()
if imageItem is None:
self.imageItem = pyqtgraph.ImageItem()
else:
self.imageItem = imageItem
self.view.addItem(self.imageItem)
self.currentIndex = 0
self.ui.histogram.setImageItem(self.imageItem)
self.keysPressed = {}
## wrap functions from view box
for fn in ['addItem', 'removeItem']:
setattr(self, fn, getattr(self.view, fn))
## wrap functions from histogram
for fn in ['setHistogramRange', 'autoHistogramRange', 'getLookupTable', 'getLevels']:
setattr(self, fn, getattr(self.ui.histogram, fn))
self.noRepeatKeys = [QtCore.Qt.Key_Right, QtCore.Qt.Key_Left, QtCore.Qt.Key_Up, QtCore.Qt.Key_Down, QtCore.Qt.Key_PageUp, QtCore.Qt.Key_PageDown]
def setImage(self, img, autoRange=True, autoLevels=True, levels=None, axes=None, xvals=None, pos=None, scale=None, transform=None, autoHistogramRange=True):
"""
Set the image to be displayed in the widget.
================== =======================================================================
**Arguments:**
img (numpy array) the image to be displayed.
xvals (numpy array) 1D array of z-axis values corresponding to the third axis
in a 3D image. For video, this array should contain the time of each frame.
autoRange (bool) whether to scale/pan the view to fit the image.
autoLevels (bool) whether to update the white/black levels to fit the image.
levels (min, max); the white and black level values to use.
axes Dictionary indicating the interpretation for each axis.
This is only needed to override the default guess. Format is::
{'t':0, 'x':1, 'y':2, 'c':3};
pos Change the position of the displayed image
scale Change the scale of the displayed image
transform Set the transform of the displayed image. This option overrides *pos*
and *scale*.
autoHistogramRange If True, the histogram y-range is automatically scaled to fit the
image data.
================== =======================================================================
"""
if hasattr(img, 'implements') and img.implements('MetaArray'):
img = img.asarray()
if not isinstance(img, numpy.ndarray):
raise Exception("Image must be specified as ndarray.")
self.image = img
if xvals is not None:
self.tVals = xvals
elif hasattr(img, 'xvals'):
try:
self.tVals = img.xvals(0)
except:
self.tVals = numpy.arange(img.shape[0])
else:
self.tVals = numpy.arange(img.shape[0])
if axes is None:
if img.ndim == 2:
self.axes = {'t': None, 'x': 0, 'y': 1, 'c': None}
elif img.ndim == 3:
if img.shape[2] <= 4:
self.axes = {'t': None, 'x': 0, 'y': 1, 'c': 2}
else:
self.axes = {'t': 0, 'x': 1, 'y': 2, 'c': None}
elif img.ndim == 4:
self.axes = {'t': 0, 'x': 1, 'y': 2, 'c': 3}
else:
raise Exception("Can not interpret image with dimensions %s" % (str(img.shape)))
elif isinstance(axes, dict):
self.axes = axes.copy()
elif isinstance(axes, list) or isinstance(axes, tuple):
self.axes = {}
for i in range(len(axes)):
self.axes[axes[i]] = i
else:
raise Exception("Can not interpret axis specification %s. Must be like {'t': 2, 'x': 0, 'y': 1} or ('t', 'x', 'y', 'c')" % (str(axes)))
for x in ['t', 'x', 'y', 'c']:
self.axes[x] = self.axes.get(x, None)
self.imageDisp = None
self.currentIndex = 0
self.updateImage(autoHistogramRange=autoHistogramRange)
if levels is None and autoLevels:
self.autoLevels()
if levels is not None: ## this does nothing since getProcessedImage sets these values again.
self.setLevels(*levels)
if self.axes['t'] is not None:
if len(self.tVals) > 1:
start = self.tVals.min()
stop = self.tVals.max() + abs(self.tVals[-1] - self.tVals[0]) * 0.02
elif len(self.tVals) == 1:
start = self.tVals[0] - 0.5
stop = self.tVals[0] + 0.5
else:
start = 0
stop = 1
self.imageItem.resetTransform()
if scale is not None:
self.imageItem.scale(*scale)
if pos is not None:
self.imageItem.setPos(*pos)
if transform is not None:
self.imageItem.setTransform(transform)
if autoRange:
self.autoRange()
def autoLevels(self):
"""Set the min/max intensity levels automatically to match the image data."""
self.setLevels(self.levelMin, self.levelMax)
def setLevels(self, min, max):
"""Set the min/max (bright and dark) levels."""
self.ui.histogram.setLevels(min, max)
def autoRange(self):
"""Auto scale and pan the view around the image."""
image = self.getProcessedImage()
self.view.autoRange()
def getProcessedImage(self):
"""Returns the image data after it has been processed by any normalization options in use.
This method also sets the attributes self.levelMin and self.levelMax
to indicate the range of data in the image."""
if self.imageDisp is None:
image = self.normalize(self.image)
self.imageDisp = image
self.levelMin, self.levelMax = list(map(float, ImageView.quickMinMax(self.imageDisp)))
return self.imageDisp
def close(self):
"""Closes the widget nicely, making sure to clear the graphics scene and release memory."""
self.ui.graphicsView.close()
self.scene.clear()
del self.image
del self.imageDisp
self.setParent(None)
def keyPressEvent(self, ev):
#print ev.key()
if ev.key() == QtCore.Qt.Key_Home:
self.setCurrentIndex(0)
ev.accept()
elif ev.key() == QtCore.Qt.Key_End:
self.setCurrentIndex(self.getProcessedImage().shape[0]-1)
ev.accept()
elif ev.key() in self.noRepeatKeys:
ev.accept()
if ev.isAutoRepeat():
return
self.keysPressed[ev.key()] = 1
self.evalKeyState()
else:
QtGui.QWidget.keyPressEvent(self, ev)
def keyReleaseEvent(self, ev):
if ev.key() in [QtCore.Qt.Key_Space, QtCore.Qt.Key_Home, QtCore.Qt.Key_End]:
ev.accept()
elif ev.key() in self.noRepeatKeys:
ev.accept()
if ev.isAutoRepeat():
return
try:
del self.keysPressed[ev.key()]
except:
self.keysPressed = {}
self.evalKeyState()
else:
QtGui.QWidget.keyReleaseEvent(self, ev)
def evalKeyState(self):
if len(self.keysPressed) == 1:
key = list(self.keysPressed.keys())[0]
if key == QtCore.Qt.Key_Right:
self.jumpFrames(1)
elif key == QtCore.Qt.Key_Left:
self.jumpFrames(-1)
elif key == QtCore.Qt.Key_Up:
self.jumpFrames(-10)
elif key == QtCore.Qt.Key_Down:
self.jumpFrames(10)
elif key == QtCore.Qt.Key_PageUp:
self.jumpFrames(-100)
elif key == QtCore.Qt.Key_PageDown:
self.jumpFrames(100)
def setCurrentIndex(self, ind, autoHistogramRange=True):
"""Set the currently displayed frame index."""
self.currentIndex = numpy.clip(ind, 0, self.getProcessedImage().shape[0]-1)
self.updateImage(autoHistogramRange=autoHistogramRange)
def jumpFrames(self, n):
"""Move video frame ahead n frames (may be negative)"""
if self.axes['t'] is not None:
self.setCurrentIndex(self.currentIndex + n)
self._parent.replot()
def hasTimeAxis(self):
return 't' in self.axes and self.axes['t'] is not None
@staticmethod
def quickMinMax(data):
while data.size > 1e6:
ax = numpy.argmax(data.shape)
sl = [slice(None)] * data.ndim
sl[ax] = slice(None, None, 2)
data = data[sl]
return data.min(), data.max()
def normalize(self, image):
return image
def updateImage(self, autoHistogramRange=True):
## Redraw image on screen
if self.image is None:
return
image = self.getProcessedImage()
if autoHistogramRange:
self.ui.histogram.setHistogramRange(self.levelMin, self.levelMax)
if self.axes['t'] is None:
self.imageItem.updateImage(image)
else:
self.imageItem.updateImage(image[self.currentIndex])
def getView(self):
"""Return the ViewBox (or other compatible object) which displays the ImageItem"""
return self.view
def getImageItem(self):
"""Return the ImageItem for this ImageView."""
return self.imageItem
def getHistogramWidget(self):
"""Return the HistogramLUTWidget for this ImageView"""
return self.ui.histogram
class ZmqSocket(QtCore.QObject):
"""Wrapper around a zmq socket. Provides Qt signal handling"""
ready_read = QtCore.Signal()
ready_write = QtCore.Signal()
def __init__(self, _type, parent=None, **kwargs):
QtCore.QObject.__init__(self, parent, **kwargs)
ctx = ZmqContext.instance()
self._socket = ctx.socket(_type)
fd = self._socket.getsockopt(FD)
self._notifier = QtCore.QSocketNotifier(fd, QtCore.QSocketNotifier.Read, self)
self._notifier.activated.connect(self.activity)
self._socket.setsockopt(RCVHWM, 100)
self.filters = []
def __del__(self):
"""Close socket on deletion"""
self._socket.close()
def set_identity(self, name):
"""Set zmq socket identity"""
self._socket.setsockopt(IDENTITY, name)
def identity(self):
"""Return the zmq socket identity"""
return self._socket.getsockopt(IDENTITY)
def subscribe(self, title):
"""Subscribe to a broadcast with the given title"""
# only subscribe if we're not already subscribed
if title in self.filters:
return
# scramble the filter to avoid spurious matches (like CCD matching CCD1)
m = hashlib.md5()
m.update(title.encode('UTF-8'))
self._socket.setsockopt(SUBSCRIBE, m.digest())
self.filters.append(title)
def unsubscribe(self, title):
"""Unsubscribe to a broadcast with the given title"""
m = hashlib.md5()
m.update(title.encode('UTF-8'))
self._socket.setsockopt(UNSUBSCRIBE, m.digest())
self.filters.remove(title)
def bind(self, addr):
"""Bind socket to address"""
self._socket.bind(addr)
def connect_socket(self, addr, tunnel=None):
"""Connect socket to endpoint, possible using an ssh tunnel
The tunnel argument specifies the hostname of the ssh server to
tunnel through.
Note that this still succeeds even if there's no ZMQ server on
the other end as the connection is asynchronous. For more details
check the zmq_connect(3) documentation.
"""
if(tunnel):
from zmq import ssh
# If there's no ssh server listening we're gonna
# get stuck here for a long time as there's no timeout
ssh.tunnel_connection(self._socket, addr, tunnel)
else:
self._socket.connect(addr)
def activity(self):
"""Callback run when there's activity on the socket"""
self._notifier.setEnabled(False)
while(self._socket.getsockopt(EVENTS) & POLLIN):
self.ready_read.emit()
self._notifier.setEnabled(True)
def recv(self, flags=0):
"""Receive a message on the socket"""
return self._socket.recv(flags)
def recv_json(self, flags=0):
"""Receive and json decode a message on the socket"""
return self._socket.recv_json(flags)
def recv_multipart(self):
"""Receive a multipart message on the socket"""
return self._socket.recv_multipart()
def send(self, _msg):
"""Send a message on the socket"""
return self._socket.send(_msg)
def send_multipart(self, _msg):
"""Send a list of messages as a multipart message on the socket"""
return self._socket.send_multipart(_msg)
def recv_array(self, flags=0, copy=True, track=False):
"""Receive a numpy array"""
md = self._socket.recv_json(flags=flags)
msg = self._socket.recv(flags=flags, copy=copy, track=track)
return numpy.ndarray(shape=md['shape'], dtype=md['dtype'], buffer=msg, strides=md['strides'])