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Refactor volume consensus #928

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Refactor volume consensus #928

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fe10654
Using DWT instead of SWT
Oct 10, 2024
742d7a8
Added difference output
Oct 22, 2024
ce29873
Merge branch 'devel' into olz_volume_consensus
oierlauzi Oct 22, 2024
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110 changes: 83 additions & 27 deletions src/xmipp/applications/scripts/volume_consensus/volume_consensus.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,11 +27,13 @@
*
**************************************************************************
"""
from os.path import splitext
import math
import os
import itertools
import numpy as np
import pywt
import pywt.data

from scipy.ndimage import zoom
from xmipp_base import XmippScript
import xmippLib
Expand All @@ -54,51 +56,105 @@ def run(self):
outVolFn = self.getParam('-o')
self.computeVolumeConsensus(inputFile, outVolFn)

def resize(self, image, dim):
imageFt = np.fft.rfftn(image)
resultFt = np.zeros(dim[:-1] + (dim[-1]//2+1,), dtype=imageFt.dtype)

copyExtent = np.minimum(image.shape, dim) // 2
srcCornerStart = image.shape-copyExtent
dstCornerStart = dim-copyExtent
for corners in itertools.product(range(2), repeat=len(dim)-1):
corners = np.array(corners + (0, ))
srcStart = np.where(corners, srcCornerStart, 0)
srcEnd = srcStart + copyExtent
dstStart = np.where(corners, dstCornerStart, 0)
dstEnd = dstStart + copyExtent
srcSlices = [slice(s, e) for s, e in zip(srcStart, srcEnd)]
dstSlices = [slice(s, e) for s, e in zip(dstStart, dstEnd)]
resultFt[tuple(dstSlices)] = imageFt[tuple(srcSlices)]

return np.fft.irfftn(resultFt)

def computeVolumeConsensus(self, inputFile, outVolFn, wavelet='sym11'):
outputWt = None
outputMin = None
xdim2 = None
xdimOrig = None
image = xmippLib.Image()
with open(inputFile) as f:
for line in f:
fileName = line.split()[0]
if fileName.endswith('.mrc'):
fileName += ':mrc'
V = xmippLib.Image(fileName)
vol = V.getData()

image.read(fileName)
volume = image.getData()

if xdimOrig is None:
xdimOrig = vol.shape[0]
xdim2 = 2**(math.ceil(math.log(xdimOrig, 2))) # Next power of 2
ydimOrig = vol.shape[1]
ydim2 = 2 ** (math.ceil(math.log(ydimOrig, 2))) # Next power of 2
zdimOrig = vol.shape[2]
zdim2 = 2 ** (math.ceil(math.log(zdimOrig, 2))) # Next power of 2
xdimOrig = volume.shape[0]
xdim2 = 2**(math.ceil(math.log2(xdimOrig))) # Next power of 2
ydimOrig = volume.shape[1]
ydim2 = 2**(math.ceil(math.log2(ydimOrig))) # Next power of 2
zdimOrig = volume.shape[2]
zdim2 = 2**(math.ceil(math.log2(zdimOrig))) # Next power of 2

if xdimOrig!=xdim2 or ydimOrig!=ydim2 or zdimOrig!=zdim2:
vol = zoom(vol, (xdim2/xdimOrig,ydim2/ydimOrig,zdim2/zdimOrig))
nlevel = pywt.swt_max_level(len(vol))
wt = pywt.swtn(vol, wavelet, nlevel, 0)
#volume = zoom(volume, (xdim2/xdimOrig,ydim2/ydimOrig,zdim2/zdimOrig))
volume = self.resize(volume, (zdim2, ydim2, xdim2))

nlevel = pywt.dwtn_max_level(volume.shape, wavelet=wavelet)
wt = pywt.wavedecn(
data=volume,
wavelet=wavelet,
level=nlevel
)

if outputWt == None:
outputWt = wt
outputMin = wt[0]['aaa']*0
outputMin = np.zeros_like(volume)
else:
for level in range(0, nlevel):
diff = np.abs(np.abs(wt[0]) - np.abs(outputWt[0]))
diff = self.resize(diff, outputMin.shape)
np.maximum(
diff, outputMin,
out=outputMin
)
outputWt[0] = np.where(
np.abs(wt[0]) > np.abs(outputWt[0]),
wt[0], outputWt[0]
)

for level in range(1, nlevel+1):
wtLevel = wt[level]
outputWtLevel = outputWt[level]
for key in wtLevel:
outputWtLevel[key] = np.where(np.abs(outputWtLevel[key]) > np.abs(wtLevel[key]),
outputWtLevel[key], wtLevel[key])
diff = np.abs(np.abs(outputWtLevel[key]) - np.abs(wtLevel[key]))
outputMin = np.where(outputMin > diff, outputMin, diff)
for detail in wtLevel:
wtLevelDetail = wtLevel[detail]
outputWtLevelDetail = outputWtLevel[detail]

diff = np.abs(np.abs(wtLevelDetail) - np.abs(outputWtLevelDetail))
diff = self.resize(diff, outputMin.shape)
np.maximum(
diff, outputMin,
out=outputMin
)

outputWtLevelDetail[...] = np.where(
np.abs(wtLevelDetail) > np.abs(outputWtLevelDetail),
wtLevelDetail, outputWtLevelDetail
)


f.close()
consensus = pywt.iswtn(outputWt, wavelet)
consensus = pywt.waverecn(outputWt, wavelet)
if xdimOrig!=xdim2 or ydimOrig!=ydim2 or zdimOrig!=zdim2:
consensus = self.resize(consensus, (zdimOrig, ydimOrig, xdimOrig))
image.setData(consensus)
image.write(outVolFn)
if xdimOrig!=xdim2 or ydimOrig!=ydim2 or zdimOrig!=zdim2:
consensus = zoom(consensus, (xdimOrig/xdim2,ydimOrig/ydim2,zdimOrig/zdim2))
V = xmippLib.Image()
V.setData(consensus)
V.write(outVolFn)
V.setData(outputMin)
outVolFn2 = splitext(outVolFn)[0] + '_diff.mrc'
V.write(outVolFn2)
outputMin = self.resize(outputMin, (zdimOrig, ydimOrig, xdimOrig))
image.setData(outputMin)
outVolFn2 = os.path.splitext(outVolFn)[0] + '_diff.mrc'
image.write(outVolFn2)


if __name__=="__main__":
Expand Down