<div dir="ltr"><p class="MsoNormal">Hi Juan, Hi Imanol,<span></span></p><p class="MsoNormal"><br></p><p class="MsoNormal">Thank you so much for your replies, which are very helpful.<span></span></p><p class="MsoNormal"><br></p><p class="MsoNormal">During saving the image, I got some warning messages such as
follows. What does it indicate?<span></span></p><p class="MsoNormal">/development/lib/python3.4/site-packages/scikit_image-0.12.3-py3.4-linux-x86_64.egg/skimage/io/_io.py:132:
UserWarning: /data/train/image_sampled.tif is a low contrast image <span></span></p><p class="MsoNormal"> warn('%s is a low
contrast image' % fname)</p><p class="MsoNormal"><span></span><br>Thanks,<span></span></p><p class="MsoNormal">Yuanyuan</p></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Dec 7, 2016 at 4:54 AM, Imanol Luengo <span dir="ltr"><<a href="mailto:imanol.luengo@nottingham.ac.uk" target="_blank">imanol.luengo@nottingham.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<p>Hello, <br>
</p>
<p>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</p>
```<br>
import numpy as np<br>
from skimage import io, util<br>
<br>
A = np.random.rand(100,100)<br>
io.imsave('tmp.png', A)<br>
B = util.img_as_float(io.imread('<wbr>tmp.png')<br>
<br>
assert np.allclose(A, B) # ERROR<br>
```
<p>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:</p>
```<br>
import numpy as np<br>
<br>
A = np.random.rand(100,100)<br>
np.save('tmp.npy', A)<br>
B = np.load('tmp.npy')<br>
<br>
assert np.allclose(A, B) # True<br>
```<br>
<p>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:</p>
```<br>
A = np.random.rand(100,100)<br>
io.imsave('tmp.tif', A)<br>
B = io.imread('tmp.tif')<br>
<br>
assert np.allclose(A, B) # True<br>
```<br>
<p>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).<br>
</p>
<p>Hope it helps,</p>
<p>Imanol<br>
</p><div><div class="h5">
<br>
<div class="m_-6762154443968081140moz-cite-prefix">On 07/12/16 04:41, wine lover wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<div dir="ltr">
<p class="MsoNormal"><font color="#242729"><span style="font-size:15.3333px">Dear All, </span></font></p>
<p class="MsoNormal"><font color="#242729"><span style="font-size:15.3333px"><br>
</span></font></p>
<p class="MsoNormal"><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">In
a program, I generate an numpy array, with shape (128,128),
which is supposed to represent an image. <span></span></span></p>
<p class="MsoNormal"><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">For
instance, I have<span class="m_-6762154443968081140gmail-apple-converted-space"> </span>an
array </span><code><span style="font-size:10pt;line-height:115%;font-family:consolas;color:rgb(36,39,41);border:1pt none windowtext;padding:0in;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;background-color:rgb(239,240,241)">temp_mask</span></code><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">,
which is of type<span class="m_-6762154443968081140gmail-apple-converted-space"> </span></span><code style="white-space:pre-wrap"><span style="font-size:10pt;line-height:115%;font-family:consolas;color:rgb(36,39,41);border:1pt none windowtext;padding:0in;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;background-color:rgb(239,240,241)">float32 and
shape (128,128)</span></code><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">,
the maximum value is<span class="m_-6762154443968081140gmail-apple-converted-space"> </span></span><code style="white-space:pre-wrap"><span style="font-size:10pt;line-height:115%;font-family:consolas;color:rgb(36,39,41);border:1pt none windowtext;padding:0in;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;background-color:rgb(239,240,241)">1.0</span></code><span class="m_-6762154443968081140gmail-apple-converted-space"><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"> </span><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">and
the minimum value is<span class="m_-6762154443968081140gmail-apple-converted-space"> </span></span></span><code style="white-space:pre-wrap"><span style="font-size:10pt;line-height:115%;font-family:consolas;color:rgb(36,39,41);border:1pt none windowtext;padding:0in;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;background-color:rgb(239,240,241)">0.0. </span></code><span class="m_-6762154443968081140gmail-apple-converted-space"><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"> </span></span><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">I
saved it using<span class="m_-6762154443968081140gmail-apple-converted-space"> </span></span><code style="white-space:pre-wrap"><span style="font-size:10pt;line-height:115%;font-family:consolas;color:rgb(36,39,41);border:1pt none windowtext;padding:0in;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;background-color:rgb(239,240,241)">io.imsave(‘mask_image’,<wbr>temp_mask)</span></code><span class="m_-6762154443968081140gmail-apple-converted-space"><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"> </span><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">However,
after I re-opened this image using<span class="m_-6762154443968081140gmail-apple-converted-space"> </span></span></span><code style="white-space:pre-wrap"><span style="font-size:10pt;line-height:115%;font-family:consolas;color:rgb(36,39,41);border:1pt none windowtext;padding:0in;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;background-color:rgb(239,240,241)">img_mask =
io.imread(‘mask_image’)</span></code><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">.
The read image turns out to have type<span class="m_-6762154443968081140gmail-apple-converted-space"> </span></span><code style="white-space:pre-wrap"><span style="font-size:10pt;line-height:115%;font-family:consolas;color:rgb(36,39,41);border:1pt none windowtext;padding:0in;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;background-color:rgb(239,240,241)">unit16</span></code><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">,
the max value becomes<span class="m_-6762154443968081140gmail-apple-converted-space"> </span></span><code style="white-space:pre-wrap"><span style="font-size:10pt;line-height:115%;font-family:consolas;color:rgb(36,39,41);border:1pt none windowtext;padding:0in;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;background-color:rgb(239,240,241)">6553</span></code><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">5
and the min value is<span class="m_-6762154443968081140gmail-apple-converted-space"> </span></span><code style="white-space:pre-wrap"><span style="font-size:10pt;line-height:115%;font-family:consolas;color:rgb(36,39,41);border:1pt none windowtext;padding:0in;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;background-color:rgb(239,240,241)">0</span></code><span class="m_-6762154443968081140gmail-apple-converted-space"><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"> .
It seems to me that io.imsave automatically transform the
float32 array into an unit16 array.<span></span></span></span></p>
<p class="MsoNormal"><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">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<span class="m_-6762154443968081140gmail-apple-converted-space"> </span></span><code style="white-space:pre-wrap"><span style="font-size:10pt;line-height:115%;font-family:consolas;color:rgb(36,39,41);border:1pt none windowtext;padding:0in;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;background-color:rgb(239,240,241)">float32</span></code><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">
and the range of value <code><span style="font-size:10pt;line-height:115%;font-family:consolas;border:1pt none windowtext;padding:0in;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;background-color:rgb(239,240,241)">[0.0,1.0]</span></code><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">? </span><span></span></span></p>
<p class="MsoNormal"><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><br>
</span></span></p>
<p class="MsoNormal"><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;color:rgb(36,39,41);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><span style="font-size:11.5pt;line-height:115%;font-family:arial,sans-serif;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">Thank
you very much!</span></span></p>
</div>
<br>
<fieldset class="m_-6762154443968081140mimeAttachmentHeader"></fieldset>
<br>
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