Hi Dennis,
Yes, that makes sense now... and unfortunately I can't see an easy way to
plumb that into the ImageView widget. An idea though, if you look at the
code for ImageView
(http://www.pyqtgraph.org/documentation/_modules/pyqtgraph/imageview/ImageView.html#ImageView.setImage)
the image provided does not strictly need to be an numpy array (just needs
certain attributes), so perhaps you could make a shim class which
extends/mimics a numpy ndarray, catching calls to these attributes and
mapping to the appropriate disk image file.
Of course, maybe someone has already made something like this...
http://docs.dask.org/en/latest/array.html looks interesting, though I've
never used it.
Good luck!
Patrick
On Wednesday, 31 October 2018 10:59:55 UTC+10:30, Dennis Norton wrote:
>
> Thanks, Patrick.
>
> I should have been more explicit about what I was asking. The method you
> outlined I was aware of.
>
> What I'm asking has to do if you have such a large number of files or a
> single file that is so large it can't be (or is impractical to be) read
> into memory.
>
> The idea I tried, and works thus far is to use a numpy memmap object.
>
> So imagine a file "VeryLargeImageFile.img", which consists of the binary
> data of type unsigned integer (uint16). Let's say this was captured with a
> camera of format frame shape (512,640), and there are 10,000 frames stored
> in the file.
>
> fp = np.memmap('VeryLargeImageFile.img', dtype='unt16', mode='r',
> offset=0, shape=(10000,512,640))
>
> The variable can be passed to ImageView item by imv.setImage(fp).
>
> However, for 32-bit operating systems, fp would still be limited to 2Gb.
>
> So my real question is if there is a method to pass a generator which
> reads a frame at a time to the ImageView or, if I had a large list of
> binary files, could I create a generator which will cycle through reading
> each file and return a numpy array of the data read for each file.
>
> Is what I'm asking making more sense, now? If not, let me know and I'll
> try to clarify by uploading my current code.
>
> Thanks again.
>
> -Dennis
>
> On Mon, Oct 29, 2018 at 11:47 PM Patrick <[email protected]
> <javascript:>> wrote:
>
>> Hi,
>>
>> You can load images into numpy arrays (usable by ImageItem, ImageView
>> etc) using the scipy.ndimage.imread function. I think it relies on having
>> the Python Image Library (PIL) installed. A more modern version of that
>> library is Pillow, which you could also use to load image data.
>>
>> Limitations are though that the ImageView expects each image to have the
>> same dimensions.
>>
>> Simple modification of ImageView example to demonstrate (specify your
>> image files on command line).
>>
>> #!/usr/bin/env python3
>>
>>
>> import numpy as np
>> from pyqtgraph.Qt import QtCore, QtGui
>> import pyqtgraph as pg
>> from argparse import ArgumentParser
>> from scipy.ndimage import imread
>>
>> argparser = ArgumentParser(description='Load images and display using
>> pyqtgraph ImageView widget.')
>> argparser.add_argument('input_images', help='Input filename(s) of images'
>> , nargs='+')
>> args = argparser.parse_args()
>>
>> imagelist = []
>> for filename in args.input_images:
>> print("Loading {}...".format(filename))
>> image = imread(filename)
>> imagelist.append(image)
>> print('Image shape: {}{}'.format(imagelist[len(imagelist)-1].shape,
>> '' if imagelist[len(imagelist)-1].shape == imagelist[0].shape else ' *'))
>> data=np.stack([ i for i in imagelist if i.shape==imagelist[0].shape ], 0)
>> if len(args.input_images) != data.shape[0]:
>> print('Warning: Shape of all input files must match. Those marked
>> with * are skipped.')
>>
>> # Interpret image data as row-major instead of col-major
>> pg.setConfigOptions(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')
>>
>> ## Display the data
>> imv.setImage(data)
>>
>> ## Set a custom color map
>> colors = [
>> (0, 0, 0),
>> (45, 5, 61),
>> (84, 42, 55),
>> (150, 87, 60),
>> (208, 171, 141),
>> (255, 255, 255)
>> ]
>> cmap = pg.ColorMap(pos=np.linspace(0.0, 1.0, 6), color=colors)
>> imv.setColorMap(cmap)
>>
>> ## Start Qt event loop unless running in interactive mode.
>> if __name__ == '__main__':
>> import sys
>> if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'
>> ):
>> QtGui.QApplication.instance().exec_()
>>
>>
>>
>>
>> On Monday, 29 October 2018 15:20:41 UTC+10:30, Dennis Norton wrote:
>>>
>>> I'm wondering if there is a convenient way to use the ImageView class to
>>> display images either from a list of files in a directory or from a large
>>> binary file consisting of multiple frames.
>>>
>>> Could we create a generator which yields the numpy arrays to display?
>>>
>>> Thanks.
>>>
>>> --
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>
>
> --
> -Dennis
>
>
>
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