regionprops - displaying region properties
ciaran.robb at googlemail.com
ciaran.robb at googlemail.com
Tue Apr 7 16:35:09 EDT 2015
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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