def vectorize(report,
pngFolder,
svgFolder,
replace,
curve_tolerance,
line_tolerance,
bgColor='auto'):
converted = 0
skipped = 0
print('Input PNG Folder is "{}".'.format(pngFolder))
if not (op.exists(svgFolder)):
os.makedirs(svgFolder)
print('Created output folder "{}".'.format(svgFolder))
includedExtensions = ['png']
fileNames = [
fn for fn in os.listdir(pngFolder)
if any([fn.endswith(ext) for ext in includedExtensions])
]
# iterate over all png file names
for pngFile in fileNames:
baseName = op.splitext(pngFile)[0]
svgFile = baseName + '.svg'
outputFile = op.join(svgFolder, svgFile)
if op.exists(outputFile):
if not replace:
print('svg-file "{}" already exists.'.format(svgFile))
skipped += 1
continue
# background color
inputFile = op.join(pngFolder, pngFile)
if (bgColor == 'auto'):
img = scipy.misc.imread(inputFile)
bgColor = nit.autoBackgroundColor(img)
print('bgColor is {}'.format(bgColor))
elif bgColor != '':
bgColor = nit.hex2rgb(bgColor)
print('background color {}.'.format(bgColor))
# generate and save svg with mindthegap
try:
prog = op.abspath(
op.join(op.dirname(__file__), '../mindthegap/bin/mindthegap'))
cmd = [
prog, "-i", inputFile, "-o", outputFile, "-t",
str(curve_tolerance), "-s",
str(line_tolerance)
]
if bgColor is not None:
bgColor = nit.rgb2hex(bgColor, '#')
cmd.extend(["-c", bgColor])
print('Calling:\n' + ' '.join(cmd) + '\n')
ans = subprocess.check_output(cmd,
shell=False,
stderr=subprocess.STDOUT)
converted += 1
except subprocess.CalledProcessError as e:
msg = 'Subprocess "' + e.cmd[0] + '" returned code ' + str(
e.returncode) + '.\nCommand: "' + ' '.join(
e.cmd) + '"\nMessage: "' + e.output + '"'
report.error(msg)
raise
print('vector image saved to svg file "{}".'.format(svgFile))
return {'converted': converted, 'skipped': skipped}
def main(self,input_nii,slicedir,outFolder,pctile,origin,colormap,reorient,replace,boundingbox_bgcolor,count_pixels):
nii = nibabel.load(input_nii)
dir2dim = {'x':0,'y':1,'z':2,'0':0,'1':1,'2':2,'coronal':0,'saggital':1,'horizontal':2,'axial':2}
sliceDim = dir2dim[slicedir.lower()]
# Nifti data is supposed to be in RAS orientation.
# For Nifti files that violate the standard, the reorient string can be used to correct the orientation.
if reorient:
nii = nit.reorient(nii,reorient)
hdr = nii.get_header()
q = hdr.get_best_affine();
ornt = nibabel.io_orientation(q)
print('The orientation is: {}'.format(ornt))
dims0 = [int(d) for d in nii.shape if d>1]
dims = list(dims0)
for i,d in enumerate(ornt):
dims[i] = dims0[int(d[0])]
print('The dimensions are: {}'.format(dims))
numSlices = dims[sliceDim];
baseName = op.basename(input_nii)
baseName = re.sub('.gz$', '',baseName)
baseName = re.sub('.nii$', '',baseName)
if not op.exists(outFolder):
os.makedirs(outFolder)
print('Created output folder "{}".'.format(outFolder))
rgbMode = False
img_dtype = nii.get_data_dtype();
if len(dims)==4 and dims[3]==3:
rgbMode = True
elif img_dtype.names:
if len(img_dtype.names)==3:
rgbMode = 'record'
rescale = pctile is not None
fmt = 'png'
if rescale or rgbMode:
fmt = 'jpg'
filePattern = baseName+'_%04d.{}'.format(fmt)
filePattern_py = filePattern.replace('_%04d','_{:04d}')
if origin:
try:
if origin.startswith('['):
ijk0 = json.loads(origin)
elif origin == 'center':
dims = hdr.get_data_shape()
ijk0 = [dims[0]/2,dims[1]/2,dims[2]/2]
q = hdr.get_best_affine()
q[0:3,3] = -q[0:3,0:3].dot(ijk0)
hdr.set_sform(q)
except:
raise Exception('Invalid origin "{}".'.format(origin))
# save coordinate system (Right Anterior Superior) information
rasLimits = nit.rasLimits(hdr)
# Some nii files have no origin set (other than i=0, j=0, k=0)
# Use the origin parameter to overrule this.
##if origin == 'center':
## def ctr(x1,x2):
## w=x2-x1
## return -w/2,w/2
## rasLimits = [ctr(xx[0],xx[1]) for xx in rasLimits]
with open(op.join(outFolder,'raslimits.json'), 'w') as fp:
json.dump(rasLimits,fp)
slicePos = (rasLimits[sliceDim][0] + (numpy.arange(0.0,dims[sliceDim])+0.5)*(rasLimits[sliceDim][1]-rasLimits[sliceDim][0])/dims[sliceDim]).tolist()
with open(op.join(outFolder,'slicepos.json'), 'w') as fp:
json.dump(slicePos,fp)
# quit if ALL slices already exist
if not replace:
done = True
for i in range(0,numSlices):
outFile = filePattern_py.format(i)
fullFile = op.join(outFolder,outFile)
if not op.exists(fullFile):
done = False
break
if done:
return FancyDict(
filePattern = op.join(outFolder,filePattern),
rasLimits = rasLimits
)
# load image, it is needed
img = nii.get_data()
img = nibabel.apply_orientation(img,ornt)
img = numpy.squeeze(img)
if rgbMode == 'record': img = nit.record2rgb(img)
print('Nifti image loaded, shape "{}",data type "{}"'.format(dims,img.dtype))
maxSlices = 2048;
if numSlices>maxSlices:
raise Exception('Too many slices (more than '+str(maxSlices)+')');
if not rgbMode:
minmax = nit.get_limits(img)
if rescale:
minmax = nit.get_limits(img,pctile)
print('minmax {}, rescale {}'.format(minmax,rescale))
index2rgb = nit.parse_colormap(colormap,minmax)
if isinstance(index2rgb,dict):
rgbLen = len(index2rgb[index2rgb.keys()[0]])
else:
rgbLen = len(index2rgb[0])
# save index2rgb
if not rescale:
if isinstance(index2rgb,dict):
index2rgb_hex = {index:'{:02X}{:02X}{:02X}'.format(rgb[0],rgb[1],rgb[2]) for (index,rgb) in index2rgb.iteritems()}
else:
index2rgb_hex = ['{:02X}{:02X}{:02X}'.format(rgb[0],rgb[1],rgb[2]) for rgb in index2rgb]
with open(op.join(outFolder,'index2rgb.json'), 'w') as fp:
json.dump(index2rgb_hex,fp)
elif rgbMode:
grayscale = img.dot(numpy.array([0.2989,0.5870,0.1140]))
minmax = nit.get_limits(grayscale)
if rescale:
minmax = nit.get_limits(grayscale,pctile)
rescale = True
rgbLen = 3
index2rgb = False
else:
rescale = False
rgbLen = 3
index2rgb = False
bbg = boundingbox_bgcolor
if bbg is '': bbg = False
if bbg:
boundingBox = {}
boundingBoxFile = op.join(outFolder,'boundingbox.json')
if op.exists(boundingBoxFile):
with open(boundingBoxFile, 'r') as fp:
boundingBox = json.load(fp)
pxc = count_pixels
if pxc:
pixCount = {};
pixCountFile = op.join(outFolder,'pixcount.json')
if op.exists(pixCountFile):
with open(pixCountFile, 'r') as fp:
pixCount = json.load(fp)
for i in range(0,numSlices):
outFile = filePattern_py.format(i)
fullFile = op.join(outFolder,outFile)
if op.exists(fullFile):
if i==0:
print('image {}{} already exists as {}-file "{}".'.format(sliceDim,i,fmt,fullFile))
if not replace:
continue
slc = nit.get_slice(img,sliceDim,i)
if pxc:
labels = numpy.unique(slc)
cnt = {}
for b in labels:
cnt[str(b)] = numpy.count_nonzero(slc == b)
pixCount[i] = cnt
if index2rgb:
slc = nit.slice2rgb(slc,index2rgb,rescale,minmax[0],minmax[1])
elif rescale:
slc = nit.rgbslice_rescale(slc,minmax[0],minmax[1])
# Save image
ans = scipy.misc.toimage(slc).save(op.join(outFolder,outFile))
if bbg:
if(bbg == "auto"):
# do this only once
bgColor = nit.autoBackgroundColor(slc)
print('boundingbox auto bgColor is {}'.format(bgColor))
else:
bgColor = nit.hex2rgb(bgg)
mask = nit.imageMask(slc,[bgColor])
print 'mask shape {} {}'.format(bgColor,mask.shape)
## bounding box
nonzero = numpy.argwhere(mask)
#print 'nonzero {}'.format(nonzero)
if nonzero.size>0:
lefttop = nonzero.min(0)[::-1] # because y=rows and x=cols
rightbottom = nonzero.max(0)[::-1]
bb = lefttop.tolist()
bb.extend(rightbottom-lefttop+(1,1))
boundingBox[i] = bb
if i==0:
print('image {}{} saved to {}-file "{}".'.format(sliceDim,i,fmt,fullFile))
if bbg:
if len(boundingBox)>0:
bb0 = boundingBox.itervalues().next()
xyMin = [bb0[0],bb0[1]]
xyMax = [bb0[0]+bb0[2],bb0[1]+bb0[3]]
for bb in boundingBox.itervalues():
if bb[0]<xyMin[0]: xyMin[0] = bb[0]
if bb[1]<xyMin[1]: xyMin[1] = bb[1]
if bb[0]+bb[2]>xyMax[0]: xyMax[0] = bb[0]+bb[2]
if bb[1]+bb[3]>xyMax[1]: xyMax[1] = bb[1]+bb[3]
boundingBox['combined'] = [xyMin[0],xyMin[1],xyMax[0]-xyMin[0],xyMax[1]-xyMin[1]]
with open(boundingBoxFile, 'w') as fp:
json.dump(boundingBox,fp)
if pxc:
with open(pixCountFile, 'w') as fp:
json.dump(pixCount,fp)
return FancyDict(
filePattern=op.join(outFolder,filePattern),
rasLimits=rasLimits
)
def run(args):
try:
skipped = 0
print('Input PNG Folder: ' + args.png_src)
pngFolder = args.png_src
svgFolder = args.svg_dest
if not (op.exists(svgFolder)):
os.makedirs(svgFolder)
print 'Created output folder "{}".'.format(svgFolder)
# generate hulls in temp dir
tmpdir = tempfile.mkdtemp(prefix='hull')
includedExtensions = ['png']
fileNames = [
fn for fn in os.listdir(pngFolder)
if any([fn.endswith(ext) for ext in includedExtensions])
]
for pngFile in fileNames:
svgFile = op.splitext(pngFile)[0] + '.svg'
outputFile = op.join(svgFolder, svgFile)
if op.exists(outputFile):
if not args.replace:
print('Skipping svg-hull "{}", it already exists.'.format(
svgFile))
skipped += 1
continue
img = scipy.misc.imread(op.join(pngFolder, pngFile))
# ignore alpha
if img.shape[-1] == 4:
if len(img.shape) == 3:
img = img[:, :, 0:3]
elif len(img.shape) == 4:
img = img[:, :, :, 0:3]
if (args.bg_color == "auto"):
bgColor = nit.autoBackgroundColor(img)
print('bgColor is {}'.format(bgColor))
else:
bgColor = nit.hex2rgb(args.bg_color)
if img.shape[-1] == 4: bgColor.append(255)
mask = nit.imageMask(img, [bgColor])
print 'mask shape {}'.format(mask.shape)
hullFile = op.join(tmpdir, pngFile)
if numpy.any(mask):
print 'Computing convex hull for image "{}"'.format(hullFile)
hull = convex_hull_image(mask)
else:
hull = mask
scipy.misc.toimage(hull).save(hullFile)
print('vector image saved to svg file "{}".'.format(svgFile))
# do the svg conversion
result = png2svg.vectorize(report,
tmpdir,
svgFolder,
args.replace,
args.curve_tolerance,
args.line_tolerance,
bgColor='#000000')
# cleanup
for fn in os.listdir(tmpdir):
os.remove(op.join(tmpdir, fn))
os.rmdir(tmpdir)
result['skipped'] = skipped
report.success(result)
except:
report.fail(__file__)