regionprops - displaying region properties
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?
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...@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?
That sounds great. Would you be willing to work on integrating this into skimage? Thanks.
On Feb 26, 2015, at 11:51 AM, ciaran.robb@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...@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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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...@googlemail.com <javascript:> 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...@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?
-- You received this message because you are subscribed to the Google Groups "scikit-image" group. To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image...@googlegroups.com <javascript:>. For more options, visit https://groups.google.com/d/optout.
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, ciaran.robb@googlemail.com 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...@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...@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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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...@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...@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...@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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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@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...@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...@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...@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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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...@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...@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...@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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participants (3)
-
ciaran.robb＠googlemail.com -
Johannes Schoenberger -
Juan Nunez-Iglesias