error: could not convert string to float (CordZ)

Question

I am trying to extract nodule patches from CT images based on the co-ordinates given in a CSV file. i keep getting this error msg at the worldcoord line :could not convert string to float(CordZ). I am not quite sure how to do that.

I have this so far:

def readCSV(filename):

    def readCSV(filename): lines = []
    with open(filename, 'r') as f:
        csvreader = csv.reader(f)
        for line in csvreader:
            lines.append(line)
    return lines

    cands = readCSV(cand_path)

    for cand in cands: 
        worldCoord = np.asarray([float(cand[3]),float(cand[2]),float(cand[1])])
        voxelCoord = worldToVoxelCoord(worldCoord, numpyOrigin, numpySpacing)
        voxelWidth = 65
        patch = numpyImage[voxelCoord[0],voxelCoord[1]-voxelWidth/2:voxelCoord[1]+voxelWidth/2,voxelCoord[2]-voxelWidth/2:voxelCoord[2]+voxelWidth/2]
        patch = normalizePlanes(patch)
        print ('data')
        print (worldCoord)
        print (voxelCoord)

Could you provide example data which you try to read? Are you sure that file does not contain header that you read as a normal data instead of skipping? — trivelt, Aug 08 '17 at 07:14
Hi @jboockmann, i solved that error but i am getting new error at the patch line: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices — Anil Yadav, Aug 08 '17 at 07:17

score 0 · Answer 1 · edited Aug 09 '17 at 15:46

0

I additionally had to specify the line number for the CSV file. So Ii did:

for cand in cands[1:]

edited Aug 09 '17 at 15:46

Donald Duck

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answered Aug 08 '17 at 08:25

Anil Yadav

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score 0 · Answer 2 · answered Mar 15 '19 at 19:34

Solution for "only integers, slices (:), ellipsis (...), numpy.newaxis (None) and integer or boolean arrays are valid indices"

Change,

patch = numpyImage [voxelCoord[0],voxelCoord[1]- voxelWidth/2:voxelCoord[1]+voxelWidth/2,voxelCoord[2]-voxelWidth/2:voxelCoord[2]+voxelWidth/2]

to,

patch = numpyImage [int(voxelCoord[0]),int(voxelCoord[1])- int(voxelWidth/2):int(voxelCoord[1])+int(voxelWidth/2),int(voxelCoord[2])-int(voxelWidth/2):int(voxelCoord[2])+int(voxelWidth/2)]

error: could not convert string to float (CordZ)

2 Answers2