regionprops - displaying region properties

[ciaran.robb at googlemail.com]

Hi again,

Here is a demo of the routine using a skimage.data example. I guess it'd be 
case of incorporating the loop or something like it in somewhere....  

from skimage import graph, data,segmentation
from matplotlib import pyplot as plt
import numpy as np

#creating a segmented image
im = data.immunohistochemistry()
seg = segmentation.felzenszwalb(im, scale=200, sigma=0.7, min_size=50)
BW = segmentation.find_boundaries(seg)
im[BW==1]=0
plt.imshow(im)
plt.show()

from skimage.measure import regionprops
Props = regionprops(seg,['Area'])

#here is the code for creating the regionprops image
labels = np.unique(seg) #a vector of label vals
PropIM = np.zeros_like(seg) # allocated blank array
for label in labels:
    propval=Props[label-1]['Area'] 
    PropIM[seg==label]=propval

#for visualising with segment boundaries
PropIM[BW==1]=0

plt.imshow(PropIM, vmin=PropIM.min(), vmax=PropIM.max())
plt.colorbar()
plt.show()


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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> > 
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>
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