Numpy/Python performing terribly vs. Matlab
- by Nissl
Novice programmer here. I'm writing a program that analyzes the relative spatial locations of points (cells). The program gets boundaries and cell type off an array with the x coordinate in column 1, y coordinate in column 2, and cell type in column 3. It then checks each cell for cell type and appropriate distance from the bounds. If it passes, it then calculates its distance from each other cell in the array and if the distance is within a specified analysis range it adds it to an output array at that distance.
My cell marking program is in wxpython so I was hoping to develop this program in python as well and eventually stick it into the GUI. Unfortunately right now python takes ~20 seconds to run the core loop on my machine while MATLAB can do ~15 loops/second. Since I'm planning on doing 1000 loops (with a randomized comparison condition) on ~30 cases times several exploratory analysis types this is not a trivial difference.
I tried running a profiler and array calls are 1/4 of the time, almost all of the rest is unspecified loop time.
Here is the python code for the main loop:
for basecell in range (0, cellnumber-1):
if firstcelltype == np.array((cellrecord[basecell,2])):
xloc=np.array((cellrecord[basecell,0]))
yloc=np.array((cellrecord[basecell,1]))
xedgedist=(xbound-xloc)
yedgedist=(ybound-yloc)
if xloc>excludedist and xedgedist>excludedist and yloc>excludedist and yedgedist>excludedist:
for comparecell in range (0, cellnumber-1):
if secondcelltype==np.array((cellrecord[comparecell,2])):
xcomploc=np.array((cellrecord[comparecell,0]))
ycomploc=np.array((cellrecord[comparecell,1]))
dist=math.sqrt((xcomploc-xloc)**2+(ycomploc-yloc)**2)
dist=round(dist)
if dist>=1 and dist<=analysisdist:
arraytarget=round(dist*analysisdist/intervalnumber)
addone=np.array((spatialraw[arraytarget-1]))
addone=addone+1
targetcell=arraytarget-1
np.put(spatialraw,[targetcell,targetcell],addone)
Here is the matlab code for the main loop:
for basecell = 1:cellnumber;
if firstcelltype==cellrecord(basecell,3);
xloc=cellrecord(basecell,1);
yloc=cellrecord(basecell,2);
xedgedist=(xbound-xloc);
yedgedist=(ybound-yloc);
if (xloc>excludedist) && (yloc>excludedist) && (xedgedist>excludedist) && (yedgedist>excludedist);
for comparecell = 1:cellnumber;
if secondcelltype==cellrecord(comparecell,3);
xcomploc=cellrecord(comparecell,1);
ycomploc=cellrecord(comparecell,2);
dist=sqrt((xcomploc-xloc)^2+(ycomploc-yloc)^2);
if (dist>=1) && (dist<=100.4999);
arraytarget=round(dist*analysisdist/intervalnumber);
spatialsum(1,arraytarget)=spatialsum(1,arraytarget)+1;
end
end
end
end
end
end
Thanks!
