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How to access cell variables stored in .mat file using h5py module?


By : Sarah Richards
Date : September 15 2020, 09:00 AM
Hope this helps .mat file saved using -v7.3 flag (HDF5 format) uses a complex data schema that uses "object references". Object references are not the data, but a pointer to the data (in a different location). You use the object reference to get to the data (in your example, the nuc values). You can get data for the first element of nuc like this:
arr = f[ f['nuc'][0][0] ][:], or arr = f[ o3[0][0] ][:]
code :


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HDF5 file created with h5py can't be opened by h5py


By : Ambiga
Date : March 29 2020, 07:55 AM
Hope this helps Since we resolved the issue in the comments on my question, I'm writing the results out here to mark it as solved.
The main problem was that I forgot to close the file after I created it. There would have been two simple options, either:
code :
import numpy as np
import h5py

f = h5py.File('myfile.hdf5','w')
group = f.create_group('a_group')
group.create_dataset(name='matrix', data=np.zeros((10, 10)), chunks=True, compression='gzip')
f.close()
import numpy as np
import h5py

with h5py.File('myfile.hdf5','w') as f:
    group = f.create_group('a_group')
    group.create_dataset(name='matrix', data=np.zeros((10, 10)), chunks=True, compression='gzip')

Reading a Matlab's cell array saved as a v7.3 .mat file with H5py


By : user3110066
Date : March 29 2020, 07:55 AM
fixed the issue. Will look into that further I saved a cell array as a .mat file in Matlab as follows: , Writing in Matlab:
code :
test = {'Hello', 'world!'; 'Good', 'morning'; 'See', 'you!'};
save('data.mat', 'test', '-v7.3') % v7.3 so that it is readable by h5py
import h5py
import numpy as np

data = []
with h5py.File("data.mat") as f:
    for column in f['test']:
        row_data = []
        for row_number in range(len(column)):            
            row_data.append(''.join(map(unichr, f[column[row_number]][:])))   
        data.append(row_data)

print data
print np.transpose(data)
[[u'Hello', u'Good', u'See'], [u'world!', u'morning', u'you!']]

[[u'Hello' u'world!']
 [u'Good' u'morning']
 [u'See' u'you!']]

Reading ALL variables in a .mat file with python h5py


By : user3537627
Date : March 29 2020, 07:55 AM
this will help After seeing some of the comments, and the documentations for H5PY Groups, I've found that you can iterate through all of the H5PY "Items" to get the value associated to each variable name. I gave an example below. Please post if their is a better way of grabbing the variable names and values.
Note: The example only pulls the value of variables that contain numeric arrays (h5py.Dataset). If you have nested Groups or cell arrays then you need to access them further to get the values.
code :
import numpy as np
import h5py

f = h5py.File('simdata_020_01.mat','r')
variables = f.items()

for var in variables:
    name = var[0]
    data = var[1]
    print "Name ", name  # Name
    if type(data) is h5py.Dataset:
        # If DataSet pull the associated Data
        # If not a dataset, you may need to access the element sub-items
        value = data.value
        print "Value", value  # NumPy Array / Value

Adding data to existing h5py file along new axis using h5py


By : MJA
Date : March 29 2020, 07:55 AM
I wish this helpful for you Using http://docs.h5py.org/en/latest/high/dataset.html I experimented a bit:
code :
In [504]: import h5py
In [505]: f=h5py.File('data.h5','w')
In [506]: data=np.ones((3,5))
In [509]: dset=f.create_dataset('dset', data=data)
In [510]: dset.shape
Out[510]: (3, 5)
In [511]: dset.maxshape
Out[511]: (3, 5)
In [512]: dset.resize?
Signature: dset.resize(size, axis=None)
Docstring:
Resize the dataset, or the specified axis.

The dataset must be stored in chunked format; it can be resized up to
the "maximum shape" (keyword maxshape) specified at creation time.
The rank of the dataset cannot be changed.
In [513]: dset1=f.create_dataset('dset1', data=data, maxshape=(2,10,10))
...
ValueError: "maxshape" must have same rank as dataset shape
In [514]: dset1=f.create_dataset('dset1', data=data[None,...], maxshape=(2,10,10))
In [515]: dset1
Out[515]: <HDF5 dataset "dset1": shape (1, 3, 5), type "<f8">
In [517]: dset1.resize((2,3,10))
In [518]: dset1
Out[518]: <HDF5 dataset "dset1": shape (2, 3, 10), type "<f8">
In [519]: dset1[:]
Out[519]: 
array([[[ 1.,  1.,  1.,  1.,  1.,  0.,  0.,  0.,  0.,  0.],
        [ 1.,  1.,  1.,  1.,  1.,  0.,  0.,  0.,  0.,  0.],
        [ 1.,  1.,  1.,  1.,  1.,  0.,  0.,  0.,  0.,  0.]],

       [[ 0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],
        [ 0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],
        [ 0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.]]])
In [521]: dset1[1,:,:]=10
In [523]: dset1[0,:,5:]=2

In [524]: dset1[:]
Out[524]: 
array([[[  1.,   1.,   1.,   1.,   1.,   2.,   2.,   2.,   2.,   2.],
        [  1.,   1.,   1.,   1.,   1.,   2.,   2.,   2.,   2.,   2.],
        [  1.,   1.,   1.,   1.,   1.,   2.,   2.,   2.,   2.,   2.]],

       [[ 10.,  10.,  10.,  10.,  10.,  10.,  10.,  10.,  10.,  10.],
        [ 10.,  10.,  10.,  10.,  10.,  10.,  10.,  10.,  10.,  10.],
        [ 10.,  10.,  10.,  10.,  10.,  10.,  10.,  10.,  10.,  10.]]])
dataset12 = np.stack((dataset1, dataset2), axis=0)

Generate csv file for values stored in variables - Javascript and Nodejs module


By : Alexandra Riera
Date : March 29 2020, 07:55 AM
this will help I have variables as below which stores values. I want this variables to be stored as Key:Value in csv file. Need your help in doing this with javascript or node module , You can use object like:
code :
var data = {
  name: "Alex",
  Age: 25,
};

var output = [
  Object.keys(data).join(','),
  Object.values(data).join(',')
].join('\n');

console.log(output);
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