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forwardOnBigImages.py
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Fri, Apr 19, 16:00

forwardOnBigImages.py
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import numpy as np
import networkTraining.cropRoutines as cropRoutines
import torch
def targetCoords(sourceCoords,validCoords):
cc=sourceCoords
vc=validCoords
tc=[]
for i in range(len(cc)):
tc.append(slice(cc[i].start+vc[i].start,cc[i].start+vc[i].stop))
return tc
def processChunk(inChunk,cropSize,marginSize,startDim,net,outChannels=None):
nc=cropRoutines.noCrops(inChunk.shape,cropSize,marginSize,startDim)
size=np.array(inChunk.shape)
if outChannels:
size[1]=outChannels
outChunk=np.zeros(tuple(size))
net.eval()
for i in range(nc):
cc,vc=cropRoutines.cropCoords(i,cropSize,marginSize,inChunk.shape,startDim)
tc=targetCoords(cc,vc)
crop=inChunk[tuple(cc)]
o=net.forward(torch.from_numpy(crop).cuda())
tc[1]=slice(0,size[1])
vc[1]=slice(0,size[1])
outChunk[tuple(tc)]=o.cpu().data.numpy()[tuple(vc)]
return outChunk
def processChunk_v2(inChunk,cropSize,marginSize,startDim,net,outDims=None):
# outDims can be a tuple of sizes...
nc=cropRoutines.noCrops(inChunk.shape,cropSize,marginSize,startDim)
size=inChunk.shape
if outDims:
size=[]
for k in range(len(outDims)):
size.append(outDims[k])
for k in range(startDim,inChunk.ndim):
size.append(inChunk.shape[k])
outChunk=np.zeros(tuple(size))
net.eval()
for i in range(nc):
cc,vc=cropRoutines.cropCoords(i,cropSize,marginSize,inChunk.shape,startDim)
tc=targetCoords(cc,vc)
crop=inChunk[tuple(cc)]
o=net.forward(torch.from_numpy(crop).cuda())
if outDims:
ttc=[]
tvc=[]
for k in range(len(outDims)):
ttc.append(slice(0,outDims[k]))
tvc.append(slice(0,outDims[k]))
for k in range(startDim,inChunk.ndim):
ttc.append(tc[k])
tvc.append(vc[k])
tc=ttc
vc=tvc
print("osize",o.size())
print("cropshape",crop.shape)
print("tc,vc",tc,vc)
print("outchanksjape",outChunk.shape)
print("oshape",o.cpu().data.numpy().shape)
outChunk[tuple(tc)]=o.cpu().data.numpy()[tuple(vc)]
return outChunk

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