First of all thank you for sharing your tool that can reliably parse tree images. I got the image_data.treeStructure at the end with the following warnings. However, the image_data.treeStructure has no branch length (only species name and tree topology). Is the leaf length information ignored during parsing?
>>> phyloParser = PhyloParser(clfPath = clfPath)Loading classifier from model/RF.pklmodel not loaded model/RF.pkl
>>> image_data = phyloParser.includeLinesFromCorners(image_data)/home/user/lib/python2.7/site-packages/numpy/core/fromnumeric.py:3146: RuntimeWarning: Degrees of freedom <= 0 for slice **kwargs)/home/user/lib/python2.7/site-packages/numpy/core/_methods.py:105: RuntimeWarning: invalid value encountered in true_divide arrmean, rcount, out=arrmean, casting='unsafe', subok=False)/home/user/lib/python2.7/site-packages/numpy/core/_methods.py:127: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount)/home/user/lib/python2.7/site-packages/numpy/core/fromnumeric.py:2909: RuntimeWarning: Mean of empty slice. out=out, **kwargs)/home/user/lib/python2.7/site-packages/numpy/core/_methods.py:80: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount)
Hi,
First of all thank you for sharing your tool that can reliably parse tree images. I got the image_data.treeStructure at the end with the following warnings. However, the image_data.treeStructure has no branch length (only species name and tree topology). Is the leaf length information ignored during parsing?
>>> phyloParser = PhyloParser(clfPath = clfPath)Loading classifier from model/RF.pklmodel not loaded model/RF.pkl>>> image_data = phyloParser.includeLinesFromCorners(image_data)/home/user/lib/python2.7/site-packages/numpy/core/fromnumeric.py:3146: RuntimeWarning: Degrees of freedom <= 0 for slice **kwargs)/home/user/lib/python2.7/site-packages/numpy/core/_methods.py:105: RuntimeWarning: invalid value encountered in true_divide arrmean, rcount, out=arrmean, casting='unsafe', subok=False)/home/user/lib/python2.7/site-packages/numpy/core/_methods.py:127: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount)/home/user/lib/python2.7/site-packages/numpy/core/fromnumeric.py:2909: RuntimeWarning: Mean of empty slice. out=out, **kwargs)/home/user/lib/python2.7/site-packages/numpy/core/_methods.py:80: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount)