OH. Right. That's what's happening, it's not inverted, it's looping around with the overflow! (I was wondering why the correlation was not closer to -1.)

Guh. imho:

- This really shouldn't happen. The plugin selection should be aware of the data type, and use only a plugin that can handle it (if available)

- PIL can definitely do 16bit PNG, so either it is being used incorrectly, or the imsave docstring stating that PIL is the first selection is wrong. I just tested this on my PIL-based Gala library, which is 3D so it required a bit of modification:

In [66]: imio.write_png_image_stack(s[np.newaxis, ...], '~/Desktop/im%02i.png', axis=0)

In [67]: srg = imio.read_image_stack('/Users/nuneziglesiasj/Desktop/im0*.png')

In [68]: srg.shape
Out[68]: (1040, 1392)

In [69]: (s == srg).all()
Out[69]: True

- The IO module is a mess! I know Stefan mentioned overhauling it briefly, but I didn't quite realise how urgent that was. In particular:

- is `from blah import *` used as a matter of policy or is it a remnant of an earlier age? Took me ages to find the `call` function.

- `plugin_store`? I have no idea where this gets updated.

So, to the core skimage devs: what is the scope for updating this? Am I allowed to break some functionality in a PR? Or are we sticking with this API?

On Mon, May 27, 2013 at 2:32 PM, Christoph Gohlke <cjgohlke@gmail.com> wrote:

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

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