I would like to show the data of a hdf5 file in the ImageView() class from
pyqtgraph. The bare code of displaying the plot for ImageView() is:
from pyqtgraph.Qt import QtCore, QtGui
import pyqtgraph as pg
# Interpret image data as row-major instead of col-major
pg.setConfigOptions(leftButtonPan = False, imageAxisOrder='row-major')
app = QtGui.QApplication([])
## Create window with ImageView widget
win = QtGui.QMainWindow()
win.resize(800,800)
imv = pg.ImageView()
win.setCentralWidget(imv)
win.show()
win.setWindowTitle('pyqtgraph example: ImageView')
if __name__ == '__main__':
import sys
if (sys.flags.interactive != 1) or not hasattr(QtCore,
'PYQT_VERSION'):
QtGui.QApplication.instance().exec_()
There is however also a hdf5 example in the pyqtgraph example set. I'm
unfortunately not able to get it to work. I made some alterations to the
example to make it work for my needs but I'm getting an error. Here is
first the code:
import numpy as np
import h5py
import pyqtgraph as pg
from pyqtgraph.Qt import QtCore, QtGui
pg.mkQApp()
plt = pg.plot()
plt.setWindowTitle('pyqtgraph example: HDF5 big data')
plt.enableAutoRange(False, False)
plt.setXRange(0, 500)
class HDF5Plot(pg.ImageItem):
def __init__(self, *args, **kwds):
self.hdf5 = None
self.limit = 10000 # maximum number of samples to be plotted
pg.ImageItem.__init__(self, *args, **kwds)
def setHDF5(self, data):
self.hdf5 = data
self.updateHDF5Plot()
def viewRangeChanged(self):
self.updateHDF5Plot()
def updateHDF5Plot(self):
if self.hdf5 is None:
self.setData([])
return
vb = self.getViewBox()
if vb is None:
return # no ViewBox yet
# Determine what data range must be read from HDF5
xrange = vb.viewRange()[0]
start = max(0, int(xrange[0]) - 1)
stop = min(len(self.hdf5), int(xrange[1] + 2))
# Decide by how much we should downsample
ds = int((stop - start) / self.limit) + 1
if ds == 1:
# Small enough to display with no intervention.
visible = self.hdf5[start:stop]
scale = 1
else:
# Here convert data into a down-sampled array suitable for
visualizing.
# Must do this piecewise to limit memory usage.
samples = 1 + ((stop - start) // ds)
visible = np.zeros(samples * 2, dtype=self.hdf5.dtype)
sourcePtr = start
targetPtr = 0
# read data in chunks of ~1M samples
chunkSize = (1000000 // ds) * ds
while sourcePtr < stop - 1:
chunk = self.hdf5[sourcePtr:min(stop, sourcePtr +
chunkSize)]
sourcePtr += len(chunk)
# reshape chunk to be integral multiple of ds
chunk = chunk[:(len(chunk) // ds) *
ds].reshape(len(chunk) // ds, ds)
# compute max and min
chunkMax = chunk.max(axis=1)
chunkMin = chunk.min(axis=1)
# interleave min and max into plot data to preserve
envelope shape
visible[targetPtr:targetPtr + chunk.shape[0] * 2:2] =
chunkMin
visible[1 + targetPtr:1 + targetPtr + chunk.shape[0] *
2:2] = chunkMax
targetPtr += chunk.shape[0] * 2
visible = visible[:targetPtr]
scale = ds * 0.5
self.setData(visible) # update the plot
self.setPos(start, 0) # shift to match starting index
self.resetTransform()
self.scale(scale, 1) # scale to match downsampling
f = h5py.File('test.hdf5', 'r')
curve = HDF5Plot()
curve.setHDF5(f['data'])
plt.addItem(curve)
## Start Qt event loop unless running in interactive mode or using
pyside.
if __name__ == '__main__':
import sys
if (sys.flags.interactive != 1) or not hasattr(QtCore,
'PYQT_VERSION'):
QtGui.QApplication.instance().exec_()
And here is the error:
Traceback (most recent call last):
File "pyqtg.py", line 206, in <module>
curve.setHDF5(f['data'])
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File
"/home/anaconda3/envs/img/lib/python3.8/site-packages/h5py-3.3.0-py3.8-linux-x86_64.egg/h5py/_hl/group.py",
line 305, in __getitem__
oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5o.pyx", line 190, in h5py.h5o.open
KeyError: "Unable to open object (object 'data' doesn't exist)"
The problem is that I don't know what/how the hdf5 file looks so I am
unsure how to replace 'data' with the correct term or if it is completely
different in and of itself. Any help is greatly appreciated.
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