Mercurial > repos > perssond > unmicst
diff toolbox/PartitionOfImage.py @ 1:74fe58ff55a5 draft default tip
planemo upload for repository https://github.com/HMS-IDAC/UnMicst commit e14f76a8803cab0013c6dbe809bc81d7667f2ab9
| author | goeckslab |
|---|---|
| date | Wed, 07 Sep 2022 23:10:14 +0000 |
| parents | 6bec4fef6b2e |
| children |
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--- a/toolbox/PartitionOfImage.py Fri Mar 12 00:17:29 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,305 +0,0 @@ -import numpy as np -from toolbox.imtools import * -# from toolbox.ftools import * -# import sys - -class PI2D: - Image = None - PaddedImage = None - PatchSize = 128 - Margin = 14 - SubPatchSize = 100 - PC = None # patch coordinates - NumPatches = 0 - Output = None - Count = None - NR = None - NC = None - NRPI = None - NCPI = None - Mode = None - W = None - - def setup(image,patchSize,margin,mode): - PI2D.Image = image - PI2D.PatchSize = patchSize - PI2D.Margin = margin - subPatchSize = patchSize-2*margin - PI2D.SubPatchSize = subPatchSize - - W = np.ones((patchSize,patchSize)) - W[[0,-1],:] = 0 - W[:,[0,-1]] = 0 - for i in range(1,2*margin): - v = i/(2*margin) - W[i,i:-i] = v - W[-i-1,i:-i] = v - W[i:-i,i] = v - W[i:-i,-i-1] = v - PI2D.W = W - - if len(image.shape) == 2: - nr,nc = image.shape - elif len(image.shape) == 3: # multi-channel image - nz,nr,nc = image.shape - - PI2D.NR = nr - PI2D.NC = nc - - npr = int(np.ceil(nr/subPatchSize)) # number of patch rows - npc = int(np.ceil(nc/subPatchSize)) # number of patch cols - - nrpi = npr*subPatchSize+2*margin # number of rows in padded image - ncpi = npc*subPatchSize+2*margin # number of cols in padded image - - PI2D.NRPI = nrpi - PI2D.NCPI = ncpi - - if len(image.shape) == 2: - PI2D.PaddedImage = np.zeros((nrpi,ncpi)) - PI2D.PaddedImage[margin:margin+nr,margin:margin+nc] = image - elif len(image.shape) == 3: - PI2D.PaddedImage = np.zeros((nz,nrpi,ncpi)) - PI2D.PaddedImage[:,margin:margin+nr,margin:margin+nc] = image - - PI2D.PC = [] # patch coordinates [r0,r1,c0,c1] - for i in range(npr): - r0 = i*subPatchSize - r1 = r0+patchSize - for j in range(npc): - c0 = j*subPatchSize - c1 = c0+patchSize - PI2D.PC.append([r0,r1,c0,c1]) - - PI2D.NumPatches = len(PI2D.PC) - PI2D.Mode = mode # 'replace' or 'accumulate' - - def getPatch(i): - r0,r1,c0,c1 = PI2D.PC[i] - if len(PI2D.PaddedImage.shape) == 2: - return PI2D.PaddedImage[r0:r1,c0:c1] - if len(PI2D.PaddedImage.shape) == 3: - return PI2D.PaddedImage[:,r0:r1,c0:c1] - - def createOutput(nChannels): - if nChannels == 1: - PI2D.Output = np.zeros((PI2D.NRPI,PI2D.NCPI),np.float16) - else: - PI2D.Output = np.zeros((nChannels,PI2D.NRPI,PI2D.NCPI),np.float16) - if PI2D.Mode == 'accumulate': - PI2D.Count = np.zeros((PI2D.NRPI,PI2D.NCPI),np.float16) - - def patchOutput(i,P): - r0,r1,c0,c1 = PI2D.PC[i] - if PI2D.Mode == 'accumulate': - PI2D.Count[r0:r1,c0:c1] += PI2D.W - if len(P.shape) == 2: - if PI2D.Mode == 'accumulate': - PI2D.Output[r0:r1,c0:c1] += np.multiply(P,PI2D.W) - elif PI2D.Mode == 'replace': - PI2D.Output[r0:r1,c0:c1] = P - elif len(P.shape) == 3: - if PI2D.Mode == 'accumulate': - for i in range(P.shape[0]): - PI2D.Output[i,r0:r1,c0:c1] += np.multiply(P[i,:,:],PI2D.W) - elif PI2D.Mode == 'replace': - PI2D.Output[:,r0:r1,c0:c1] = P - - def getValidOutput(): - margin = PI2D.Margin - nr, nc = PI2D.NR, PI2D.NC - if PI2D.Mode == 'accumulate': - C = PI2D.Count[margin:margin+nr,margin:margin+nc] - if len(PI2D.Output.shape) == 2: - if PI2D.Mode == 'accumulate': - return np.divide(PI2D.Output[margin:margin+nr,margin:margin+nc],C) - if PI2D.Mode == 'replace': - return PI2D.Output[margin:margin+nr,margin:margin+nc] - if len(PI2D.Output.shape) == 3: - if PI2D.Mode == 'accumulate': - for i in range(PI2D.Output.shape[0]): - PI2D.Output[i,margin:margin+nr,margin:margin+nc] = np.divide(PI2D.Output[i,margin:margin+nr,margin:margin+nc],C) - return PI2D.Output[:,margin:margin+nr,margin:margin+nc] - - - def demo(): - I = np.random.rand(128,128) - # PI2D.setup(I,128,14) - PI2D.setup(I,64,4,'replace') - - nChannels = 2 - PI2D.createOutput(nChannels) - - for i in range(PI2D.NumPatches): - P = PI2D.getPatch(i) - Q = np.zeros((nChannels,P.shape[0],P.shape[1])) - for j in range(nChannels): - Q[j,:,:] = P - PI2D.patchOutput(i,Q) - - J = PI2D.getValidOutput() - J = J[0,:,:] - - D = np.abs(I-J) - print(np.max(D)) - - K = cat(1,cat(1,I,J),D) - imshow(K) - - -class PI3D: - Image = None - PaddedImage = None - PatchSize = 128 - Margin = 14 - SubPatchSize = 100 - PC = None # patch coordinates - NumPatches = 0 - Output = None - Count = None - NR = None # rows - NC = None # cols - NZ = None # planes - NRPI = None - NCPI = None - NZPI = None - Mode = None - W = None - - def setup(image,patchSize,margin,mode): - PI3D.Image = image - PI3D.PatchSize = patchSize - PI3D.Margin = margin - subPatchSize = patchSize-2*margin - PI3D.SubPatchSize = subPatchSize - - W = np.ones((patchSize,patchSize,patchSize)) - W[[0,-1],:,:] = 0 - W[:,[0,-1],:] = 0 - W[:,:,[0,-1]] = 0 - for i in range(1,2*margin): - v = i/(2*margin) - W[[i,-i-1],i:-i,i:-i] = v - W[i:-i,[i,-i-1],i:-i] = v - W[i:-i,i:-i,[i,-i-1]] = v - - PI3D.W = W - - if len(image.shape) == 3: - nz,nr,nc = image.shape - elif len(image.shape) == 4: # multi-channel image - nz,nw,nr,nc = image.shape - - PI3D.NR = nr - PI3D.NC = nc - PI3D.NZ = nz - - npr = int(np.ceil(nr/subPatchSize)) # number of patch rows - npc = int(np.ceil(nc/subPatchSize)) # number of patch cols - npz = int(np.ceil(nz/subPatchSize)) # number of patch planes - - nrpi = npr*subPatchSize+2*margin # number of rows in padded image - ncpi = npc*subPatchSize+2*margin # number of cols in padded image - nzpi = npz*subPatchSize+2*margin # number of plns in padded image - - PI3D.NRPI = nrpi - PI3D.NCPI = ncpi - PI3D.NZPI = nzpi - - if len(image.shape) == 3: - PI3D.PaddedImage = np.zeros((nzpi,nrpi,ncpi)) - PI3D.PaddedImage[margin:margin+nz,margin:margin+nr,margin:margin+nc] = image - elif len(image.shape) == 4: - PI3D.PaddedImage = np.zeros((nzpi,nw,nrpi,ncpi)) - PI3D.PaddedImage[margin:margin+nz,:,margin:margin+nr,margin:margin+nc] = image - - PI3D.PC = [] # patch coordinates [z0,z1,r0,r1,c0,c1] - for iZ in range(npz): - z0 = iZ*subPatchSize - z1 = z0+patchSize - for i in range(npr): - r0 = i*subPatchSize - r1 = r0+patchSize - for j in range(npc): - c0 = j*subPatchSize - c1 = c0+patchSize - PI3D.PC.append([z0,z1,r0,r1,c0,c1]) - - PI3D.NumPatches = len(PI3D.PC) - PI3D.Mode = mode # 'replace' or 'accumulate' - - def getPatch(i): - z0,z1,r0,r1,c0,c1 = PI3D.PC[i] - if len(PI3D.PaddedImage.shape) == 3: - return PI3D.PaddedImage[z0:z1,r0:r1,c0:c1] - if len(PI3D.PaddedImage.shape) == 4: - return PI3D.PaddedImage[z0:z1,:,r0:r1,c0:c1] - - def createOutput(nChannels): - if nChannels == 1: - PI3D.Output = np.zeros((PI3D.NZPI,PI3D.NRPI,PI3D.NCPI)) - else: - PI3D.Output = np.zeros((PI3D.NZPI,nChannels,PI3D.NRPI,PI3D.NCPI)) - if PI3D.Mode == 'accumulate': - PI3D.Count = np.zeros((PI3D.NZPI,PI3D.NRPI,PI3D.NCPI)) - - def patchOutput(i,P): - z0,z1,r0,r1,c0,c1 = PI3D.PC[i] - if PI3D.Mode == 'accumulate': - PI3D.Count[z0:z1,r0:r1,c0:c1] += PI3D.W - if len(P.shape) == 3: - if PI3D.Mode == 'accumulate': - PI3D.Output[z0:z1,r0:r1,c0:c1] += np.multiply(P,PI3D.W) - elif PI3D.Mode == 'replace': - PI3D.Output[z0:z1,r0:r1,c0:c1] = P - elif len(P.shape) == 4: - if PI3D.Mode == 'accumulate': - for i in range(P.shape[1]): - PI3D.Output[z0:z1,i,r0:r1,c0:c1] += np.multiply(P[:,i,:,:],PI3D.W) - elif PI3D.Mode == 'replace': - PI3D.Output[z0:z1,:,r0:r1,c0:c1] = P - - def getValidOutput(): - margin = PI3D.Margin - nz, nr, nc = PI3D.NZ, PI3D.NR, PI3D.NC - if PI3D.Mode == 'accumulate': - C = PI3D.Count[margin:margin+nz,margin:margin+nr,margin:margin+nc] - if len(PI3D.Output.shape) == 3: - if PI3D.Mode == 'accumulate': - return np.divide(PI3D.Output[margin:margin+nz,margin:margin+nr,margin:margin+nc],C) - if PI3D.Mode == 'replace': - return PI3D.Output[margin:margin+nz,margin:margin+nr,margin:margin+nc] - if len(PI3D.Output.shape) == 4: - if PI3D.Mode == 'accumulate': - for i in range(PI3D.Output.shape[1]): - PI3D.Output[margin:margin+nz,i,margin:margin+nr,margin:margin+nc] = np.divide(PI3D.Output[margin:margin+nz,i,margin:margin+nr,margin:margin+nc],C) - return PI3D.Output[margin:margin+nz,:,margin:margin+nr,margin:margin+nc] - - - def demo(): - I = np.random.rand(128,128,128) - PI3D.setup(I,64,4,'accumulate') - - nChannels = 2 - PI3D.createOutput(nChannels) - - for i in range(PI3D.NumPatches): - P = PI3D.getPatch(i) - Q = np.zeros((P.shape[0],nChannels,P.shape[1],P.shape[2])) - for j in range(nChannels): - Q[:,j,:,:] = P - PI3D.patchOutput(i,Q) - - J = PI3D.getValidOutput() - J = J[:,0,:,:] - - D = np.abs(I-J) - print(np.max(D)) - - pI = I[64,:,:] - pJ = J[64,:,:] - pD = D[64,:,:] - - K = cat(1,cat(1,pI,pJ),pD) - imshow(K) -