On 5/26/2013 8:31 PM, Juan Nunez-Iglesias wrote:
Hey all,
I noticed that some of my microscopy images appeared inverted after saving them with skimage.io.imsave. After some testing, here's some of the weirdness. My image is called s:
```python In [37]: np.min(s) Out[37]: 119
In [38]: np.max(s) Out[38]: 4095
In [39]: s.shape Out[39]: (1040, 1392)
In [40]: s.dtype Out[40]: dtype('uint16')
In [41]: io.imsave('/Users/nuneziglesiasj/Desktop/im.tif', s)
In [42]: sr = io.imread('/Users/nuneziglesiasj/Desktop/im.tif')
In [43]: (s == sr).all() Out[43]: Image(False, dtype=bool)
In [44]: sr.min() Out[44]: Image(0, dtype=uint8)
In [45]: sr.max() Out[45]: Image(255, dtype=uint8) ```
Ok, already this is not desirable... One would hope than an imsave followed by an imread would be a no-op, but whatever, let's accept for argument's sake that we want to limit ourselves to uint8. Here's the real downer:
```python In [46]: np.corrcoef(s.ravel(), sr.ravel()) Out[46]: array([[ 1. , -0.29849602], [-0.29849602, 1. ]]) ```
This is simply unacceptable. I haven't explored any more than this yet but maybe someone has an idea about what is going on here? If it helps, the problem is with imsave � opening the images in Apple Preview shows the inversion. I just wanted to know if it was some weird incompatibility between skimage and Preview, rather than skimage acting stupid. Sadly, it appears to be the latter.
PS: I just tested with png and get the exact same result.
Not many skimage.io plugins are capable of handling 16 bit data. Use gdal (read only), tifffile (uncompressed tiff only), or freeimage, e.g. `io.use_plugin('freeimage')` Christoph