Re: future.graph.merge_hierarchical
Hi Juan, Because Vighnesh is smarter than me :) I can't see how to obtain the intermediate merger other than to create a complete label_map at each step, which requires me to iterate over all the nodes in the graph. I sure there is enough information at node to reconstruct just local map/mask but I don't know how. Hope that clarifies. Regards, Michael. -- On 21/09/2015 8:50 am, Juan Nunez-Iglesias wrote:
Hey Michael,
I don't understand your question. Why are you traversing the graph "each time"? Vighnesh only traverses it once?
Juan.
On Sun, Sep 20, 2015 at 6:55 AM bricklemacho@gmail.com <mailto:bricklemacho@gmail.com> <bricklemacho@gmail.com <mailto:bricklemacho@gmail.com>> wrote:
Hi Vighnesh,
I am struggling with both Python and the graph stuff, hope you can help me. I have taken discussion off list.
I am using your idea in your blog: Hierarchical Merging In Action. Similar to your seg_list[] concept, I plan to store a copy of the merged regions in a list. The best place appears to be at bottom of the while loop in merge_hierarchical (about line 130 in graph_merge.py). Default plan is to duplicate Lines 132-136 of graph_merge.py to create a label map:
label_map = np.arange(labels.max() + 1) for ix, (n, d) in enumerate(rag.nodes_iter(data=True)): for label in d['labels']: label_map[label] = ix
Seems bit of an overkill to traverse the entire graph each time. Is there any other way you can suggest? All I need is a label map that consists of two labels, one being the merged region and everything else grouped/labeled as another region.
Any help appreciated.
Regards,
Michael. --
On 19/09/2015 11:51 am, Vighnesh Birodkar wrote:
Hello
I am sorry, I was mistaken, there is no way of getting the merge sequence right now without changing the source.
Thanks
On Fri, Sep 18, 2015 at 9:46 PM, bricklemacho@gmail.com <mailto:bricklemacho@gmail.com> <bricklemacho@gmail.com <mailto:bricklemacho@gmail.com>> wrote:
Hi,
My graph theory is pretty weak so I may be missing something obvious. Can you elaborate a little more on your suggestion below.
Are you saying the setting in_place=False, will the graph then retain a copy of the intermediate steps? If so how do I access these intermediate steps?
Playing around with RAG Merging example (from the skimage gallery). If set rag_copy=True, I will have the starting graph, and can use the labels returned from merge_hierarchical to see the result of final merge, but I can't see way to review the intermediate steps.
Any help appreciated,
Michael. --
On 18/09/2015 10:30 pm, Vighnesh Birodkar wrote:
Hi
Using in _ place = False, couldn't you get the entire sequence of merging from the root node ?
On 17 Sep 2015 12:59, "bricklemacho@gmail.com <mailto:bricklemacho@gmail.com>" <bricklemacho@gmail.com <mailto:bricklemacho@gmail.com>> wrote:
Setting the threshold to infinity will merge everything, but in what order are the nodes merged?
Assuming setting threshold to infinity works, I still need to save a copy of each merge. Any suggestions?
Regards,
Michael. --
On 17/09/2015 11:23 pm, Vighnesh Birodkar wrote:
Hello
Rather than creating an alternative method, you could always set the threshold to infinity. Won't that work in your case ?
Thanks Vighnesh
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Hello For the demo videos in that post I was traversing the graph at each iteration to obtain the segmentation, see 118 of graph_merge.py https://github.com/vighneshbirodkar/scikit-image/compare/vighneshbirodkar:ha... This was because I needed the entire segmentation at each step to display it. Juan, I think you mean I traverse it only once in the code on master ? For the video I was indeed traversing it each time. The nodes are merged here https://github.com/scikit-image/scikit-image/blob/master/skimage/future/grap... On line 127 you can inject your logic. So if I understand correctly, you want [src + dst](the regions being merged at that point of time) as one region and the rest of the graph as other ? label_map = np.arange(labels.max() + 1) for l in rag.node[src]['labels'] : Thanks Vighnesh On Sunday, September 20, 2015 at 10:36:36 PM UTC-4, bricklemacho wrote:
Hi Juan,
Because Vighnesh is smarter than me :)
I can't see how to obtain the intermediate merger other than to create a complete label_map at each step, which requires me to iterate over all the nodes in the graph. I sure there is enough information at node to reconstruct just local map/mask but I don't know how.
Hope that clarifies.
Regards,
Michael. --
On 21/09/2015 8:50 am, Juan Nunez-Iglesias wrote:
Hey Michael,
I don't understand your question. Why are you traversing the graph "each time"? Vighnesh only traverses it once?
Juan.
On Sun, Sep 20, 2015 at 6:55 AM <javascript:>brickl...@gmail.com <javascript:> <brickl...@gmail.com <javascript:>> wrote:
Hi Vighnesh,
I am struggling with both Python and the graph stuff, hope you can help me. I have taken discussion off list.
I am using your idea in your blog: Hierarchical Merging In Action. Similar to your seg_list[] concept, I plan to store a copy of the merged regions in a list. The best place appears to be at bottom of the while loop in merge_hierarchical (about line 130 in graph_merge.py). Default plan is to duplicate Lines 132-136 of graph_merge.py to create a label map:
label_map = np.arange(labels.max() + 1) for ix, (n, d) in enumerate(rag.nodes_iter(data=True)): for label in d['labels']: label_map[label] = ix
Seems bit of an overkill to traverse the entire graph each time. Is there any other way you can suggest? All I need is a label map that consists of two labels, one being the merged region and everything else grouped/labeled as another region.
Any help appreciated.
Regards,
Michael. --
On 19/09/2015 11:51 am, Vighnesh Birodkar wrote:
Hello
I am sorry, I was mistaken, there is no way of getting the merge sequence right now without changing the source.
Thanks
On Fri, Sep 18, 2015 at 9:46 PM, brickl...@gmail.com <javascript:> < brickl...@gmail.com <javascript:>> wrote:
Hi,
My graph theory is pretty weak so I may be missing something obvious. Can you elaborate a little more on your suggestion below.
Are you saying the setting in_place=False, will the graph then retain a copy of the intermediate steps? If so how do I access these intermediate steps?
Playing around with RAG Merging example (from the skimage gallery). If set rag_copy=True, I will have the starting graph, and can use the labels returned from merge_hierarchical to see the result of final merge, but I can't see way to review the intermediate steps.
Any help appreciated,
Michael. --
On 18/09/2015 10:30 pm, Vighnesh Birodkar wrote:
Hi
Using in _ place = False, couldn't you get the entire sequence of merging from the root node ? On 17 Sep 2015 12:59, "brickl...@gmail.com <javascript:>" < brickl...@gmail.com <javascript:>> wrote:
Setting the threshold to infinity will merge everything, but in what order are the nodes merged?
Assuming setting threshold to infinity works, I still need to save a copy of each merge. Any suggestions?
Regards,
Michael. --
On 17/09/2015 11:23 pm, Vighnesh Birodkar wrote:
Hello
Rather than creating an alternative method, you could always set the threshold to infinity. Won't that work in your case ?
Thanks Vighnesh
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Vighnesh Birodkar