Creating an image using two numpy arrays

Question

I am working on a project and I do a simulation in a program called Prismatic to get files which I want to use later, Prismatic outputs files in h5 format, which I was able to extract data out of them using Python, the simulation produces an image, which is saved in two data sets (dim1, dim2), each is a numpy array of size 219 and I having trying to create the image from them again but I am not sure how that works, I tried to stack the numpy arrays but I just get a line in the image, I just learned about numpy arrays I don't know much about them yet, can anyone help? that's my code here.

fi = h5py.File('ty.h5')
a = fi['4DSTEM_simulation']['data']['realslices']['annular_detector_depth0000']['dim1'][:]
b = fi['4DSTEM_simulation']['data']['realslices']['annular_detector_depth0000']['dim2'][:]
merge_arr = numpy.stack((a, b), axis=0)
data = Image.fromarray(merge_arr)
if data.mode != 'RGB':
    data = data.convert('RGB')

An RGB image is an array with shape (n,m,3). What is the shape of your two numpy arrays? — kevinkayaks
– kevinkayaks, Commented Jun 14, 2021 at 3:26
when I print their shape I get (219,) for both, and both have the same values for all entries, which I am guessing is because simulation output is symmetric — zzjouny
– zzjouny, Commented Jun 14, 2021 at 3:28

kevinkayaks · Accepted Answer · 2021-06-14 20:10:28Z

2

Ok Given your dataset,I managed to find an image.

from matplotlib import pyplot as plt
%matplotlib inline # remove this if you are not using a jupyter notebook
import h5py
# data link https://file.io/riS5juuYLNin

f = h5py.File('ty.h5')

realslice = (f['4DSTEM_simulation']
 ['data']
 ['realslices']
 ['annular_detector_depth0000']
 ['realslice'])[:]

plt.imshow(realslice)
#plt.show() # add this if you are not using a jupyter notebook

The real tools to figure this out were seeing what the keys were at a given level of the file f, as in f.keys() or f['4DSTEM_simulation'].keys() and so on, then looking at the shapes of the items within by exacting the available objects these keys access. Eventually I found one that was an image. I do not know anything about this data so maybe there are more. It seems your original problem isn't actually anything needing solving. Two 246x1 arrays definitely doesn't form an image in a unique way.

answered Jun 14, 2021 at 20:10

kevinkayaks

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1 Comment

zzjouny Over a year ago

That looks perfect, thank you so much, that is the expected image

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