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POMore efficient way to count intersections?
 

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  1. POMore efficient way to count intersections?
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    <p>I have a list of 300000 lists (fiber tracks), where each track is a list of (x,y,z) tuples/coordinates:</p> <pre><code>tracks= [[(1,2,3),(3,2,4),...] [(4,2,1),(5,7,3),...] ... ] </code></pre> <p>I also have a group of masks, where each mask is defined as a list of (x,y,z) tuples/coordinates: </p> <pre><code>mask_coords_list= [[(1,2,3),(8,13,4),...] [(6,2,2),(5,7,3),...] ... ] </code></pre> <p>I am trying to find, for all possible pairs of masks:</p> <ol> <li>the number of tracks that intersect each mask-mask pair (to create a connectivity matrix)</li> <li>the subset of tracks that intersect each mask, in order to add 1 to each (x,y,z) coordinate for each track in the subset (to create a "density" image)</li> </ol> <p>I'm currently doing part 1 like so:</p> <pre><code>def mask_connectivity_matrix(tracks,masks,masks_coords_list): connect_mat=zeros((len(masks),len(masks))) for track in tracks: cur=[] for count,mask_coords in enumerate(masks_coords_list): if any(set(track) &amp; set(mask_coords)): cur.append(count) for x,y in list(itertools.combinations(cur,2)): connect_mat[x,y] += 1 </code></pre> <p>and part 2 like so:</p> <pre><code>def mask_tracks(tracks,masks,masks_coords_list): vox_tracks_img=zeros((xdim,ydim,zdim,len(masks))) for track in tracks: for count,mask in enumerate(masks_coords_list): if any(set(track) &amp; set(mask)): for x,y,z in track: vox_tracks_img[x,y,z,count] += 1 </code></pre> <p>Using sets to find intersections has sped this process up significantly but both portions still take over an hour when I have a list of 70 or more masks. Is there a more efficient way to do this than iterating for each track?</p>
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    1. USMcPherrinM
    1. USjbrown
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    1. COAll the answers seems to be marginal improvements, but I think you need more than that.
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      1. USMcPherrinM
    2. COIf you could post a sample data set and the correct answers in a pastebin somewhere, you might get more help.
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      1. USJason Orendorff
    3. CODo I see that right that intersections are only defined as two coordinate tuples being the same, and not as lines between coordinates intersecting?
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      1. USSvante
 

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