regionprops - displaying region properties

[Juan Nunez-Iglesias]

Hi Ciaran,




Probably the preferred way of sharing IPython notebooks is to post them to gist.github.com and share the link from nbviewer.




There's actually a gist extension to IPython notebook that will do this automagically for you:


http://nbviewer.ipython.org/gist/minrk/4982809

(Read the whole article before doing anything!)




Juan.

On Mon, Mar 30, 2015 at 3:01 AM, null <ciaran.robb at googlemail.com> wrote:

> Hi,
> Sorry for the delay, I have been bogged down with writing papers!
> I have attached an Ipython notebook with an example routine using one of 
> the skimage.data images.
> Ciaran
> On Monday, March 2, 2015 at 11:38:21 PM UTC, Johannes Schönberger wrote:
>>
>> Maybe, there is a way to elegantly integrate this into the RegionProperty 
>> class? 
>>
>> Could you share your current implementation, so we can decide for a good 
>> strategy? 
>>
>> > On Mar 2, 2015, at 6:02 PM, ciara... at googlemail.com <javascript:> 
>> wrote: 
>> > 
>> > Hi Johannes, 
>> > 
>> > Yeah of course. Would it be best placed in module color? 
>> > 
>> > Ciaran 
>> > 
>> > On Monday, March 2, 2015 at 5:26:12 PM UTC, Johannes Schönberger wrote: 
>> > That sounds great. Would you be willing to work on integrating this into 
>> skimage? 
>> > 
>> > Thanks. 
>> > 
>> > > On Feb 26, 2015, at 11:51 AM, ciara... at googlemail.com wrote: 
>> > > 
>> > > Hi 
>> > > Adding to my own post but hey.... 
>> > > 
>> > > I have since written my own code which allows visualising of region 
>> properties (eg area, eccentricity etc) via colormap, if anyone is 
>> interested let me know! 
>> > > 
>> > > Ciaran 
>> > > 
>> > > On Sunday, February 1, 2015 at 11:45:44 PM UTC, 
>> ciara... at googlemail.com wrote: 
>> > > Hello everyone, 
>> > > 
>> > > I have recently been attempting to modify some existing skimage code 
>> to display regionprops for a labeled image  (e.g. area or eccentricity) 
>> > > 
>> > > I initially tried to translate a vectorized bit of old matlab code I 
>> had, but gave up on that and decided to alter the existing label2rgb 
>> skimage function 
>> > > 
>> > > I am attempting to change each label value to it's area property value 
>> similar to the label2rgb "avg" function. 
>> > > 
>> > > so I have: 
>> > > labels = a labeled image 
>> > > 
>> > >     out = np.zeros_like(labels) #a blank array 
>> > >     labels2 = np.unique(labels) #a vector of label vals 
>> > >     out = np.zeros_like(labels) 
>> > >     Props = regionprops(labels, ['Area']) 
>> > >     bg_label=0 
>> > >     bg = (labels2 == bg_label) 
>> > >     if bg.any(): 
>> > >         labels2 = labels2[labels2 != bg_label] 
>> > >         out[bg] = 0 
>> > >         for label in labels2: 
>> > >             mask = (labels == label).nonzero()     
>> > >             color = Props[label].area 
>> > >             out[mask] = color 
>> > > but the "out" props image does not correspond to the correct area 
>> values? 
>> > > Can anyone help me with this? 
>> > >  It also throws the following error: 
>> > > "list index out of range" 
>> > > It would certainly be useful to have a way to view the spatial 
>> distribution of label properties in this way - perhaps in a future skimage 
>> version? 
>> > > 
>> > > 
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