[scikit-image] how to correctly save an numpy array with float32 type into an image

[Imanol Luengo]

Hello,

I would say there are two differences between 'Saving the data' and 
'Displaying the data'. An image is discretized to `uint8` or `uint16` 
prior to being saved as standard formates (`.png` or `.jpg`). You could 
do something like

```
import numpy as np
from skimage import io, util

A = np.random.rand(100,100)
io.imsave('tmp.png', A)
B = util.img_as_float(io.imread('tmp.png')

assert np.allclose(A, B) # ERROR
```

But you will find some discretization errors, which makes `B != A`. 
Having said that, if you want to preserve the data in `B`, I think the 
best option is to export the data using another format, e.g. numpy arrays:

```
import numpy as np

A = np.random.rand(100,100)
np.save('tmp.npy', A)
B = np.load('tmp.npy')

assert np.allclose(A, B) # True
```

Or alternatively, if you really want to save the data in a visualizable 
format, exporting the image as `.tif` format, which preserves data 
information, should also work:

```
A = np.random.rand(100,100)
io.imsave('tmp.tif', A)
B = io.imread('tmp.tif')

assert np.allclose(A, B) # True
```

However, I would personally store my data in non-visualizable formats 
such as `.npy, .h5` (the later if you work with tons of data) as they 
usually offer another advantages (e.g. Datasets in HDF5).

Hope it helps,

Imanol


On 07/12/16 04:41, wine lover wrote:
>
> Dear All,
>
>
> In a program, I generate an numpy array, with shape (128,128), which 
> is supposed to represent an image.
>
> For instance, I havean array |temp_mask|, which is of type|float32 and 
> shape (128,128)|, the maximum value is|1.0|and the minimum value 
> is|0.0. |I saved it using|io.imsave(‘mask_image’,temp_mask)|However, 
> after I re-opened this image using|img_mask = 
> io.imread(‘mask_image’)|. The read image turns out to  have 
> type|unit16|, the max value becomes|6553|5 and the min value is|0| . 
> It seems to me that io.imsave automatically transform the float32 
> array into an unit16 array.
>
> Is it possible to save the image while keeping the original type? If 
> not, what’s the correct way to save an image represented as an array, 
> with type|float32|and the range of value |[0.0,1.0]|?
>
>
> Thank you very much!
>
>
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image





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