Commit 4c2228e1 authored by Gustavo Pinzon's avatar Gustavo Pinzon
Browse files

Merge branch 'master' of https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam into ddicTools

parents dca3b07b 3c9476e1
...@@ -46,7 +46,7 @@ def register(im1, im2, im1mask=None, PhiInit=None, PhiRigid=False, PhiInitBinRat ...@@ -46,7 +46,7 @@ def register(im1, im2, im1mask=None, PhiInit=None, PhiRigid=False, PhiInitBinRat
"Discrete correlation" can be performed by masking im1. "Discrete correlation" can be performed by masking im1.
im1 and im2 do not necessarily have to be the same size (`i.e.`, im2 can be bigger) -- this is good since there im1 and im2 do not necessarily have to be the same size (`i.e.`, im2 can be bigger) -- this is good since there
is a zone to accommodate movement. In the case of a bigger im2, im1 and im2 are centred with respect to each other. is a zone to accommodate movement. In the case of a bigger im2, im1 and im2 are assumed to be centred with respect to each other.
Parameters Parameters
---------- ----------
...@@ -139,9 +139,6 @@ def register(im1, im2, im1mask=None, PhiInit=None, PhiRigid=False, PhiInitBinRat ...@@ -139,9 +139,6 @@ def register(im1, im2, im1mask=None, PhiInit=None, PhiRigid=False, PhiInitBinRat
---- ----
This correlation was written in the style of S. Roux (especially "An extension of Digital Image Correlation for intermodality image registration") This correlation was written in the style of S. Roux (especially "An extension of Digital Image Correlation for intermodality image registration")
especially equations 12 and 13. especially equations 12 and 13.
Since we're using classical DIC (without multimodal registration) there is no need to update the gradient image,
so this is calculated once at the beginning.
""" """
# Explicitly set input images to floats # Explicitly set input images to floats
im1 = im1.astype('<f4') im1 = im1.astype('<f4')
...@@ -183,8 +180,11 @@ def register(im1, im2, im1mask=None, PhiInit=None, PhiRigid=False, PhiInitBinRat ...@@ -183,8 +180,11 @@ def register(im1, im2, im1mask=None, PhiInit=None, PhiRigid=False, PhiInitBinRat
# Automatically calculate margin if none is passed # Automatically calculate margin if none is passed
# Detect default case and calculate maring necessary for a 45deg rotation with no displacement # Detect default case and calculate maring necessary for a 45deg rotation with no displacement
if margin is None: if margin is None:
# sqrt if twoD:
margin = [1+int(0.1 * max(im1.shape))] * 3 # z-margin will be overwritten below
margin = [1+int(0.1 * min(im1.shape[1:]))] * 3
else:
margin = [1+int(0.1 * min(im1.shape))] * 3
elif type(margin) == list: elif type(margin) == list:
pass pass
else: else:
......
...@@ -443,7 +443,11 @@ def registerOnGrid(im1, im2, nodePositions, halfWindowSize, PhiField=None, margi ...@@ -443,7 +443,11 @@ def registerOnGrid(im1, im2, nodePositions, halfWindowSize, PhiField=None, margi
numberOfNodes = nodePositions.shape[0] numberOfNodes = nodePositions.shape[0]
def getImagettes(nodeNumber, im1, im2, PhiField, nodePositions, margin, halfWindowSize, greyThreshold, im1mask, minMaskVolume): def getImagettes(nodeNumber, im1, im2, PhiField, nodePositions, margin, halfWindowSize, greyThreshold, im1mask, minMaskVolume, twoD=False):
# We don't have many single letter variable names, but this is one to keep things aligned
# This variable is =0 in 2D and =1 in 3D
if twoD: m = 0
else: m = 1
# Initialise defaults # Initialise defaults
imagette1mask = None imagette1mask = None
PhiInit = None PhiInit = None
...@@ -459,7 +463,7 @@ def registerOnGrid(im1, im2, nodePositions, halfWindowSize, PhiField=None, margi ...@@ -459,7 +463,7 @@ def registerOnGrid(im1, im2, nodePositions, halfWindowSize, PhiField=None, margi
#slice(int(nodePositions[nodeNumber, 1] - halfWindowSize[1] - 1), int(nodePositions[nodeNumber, 1] + halfWindowSize[1] + 1 + 1)), #slice(int(nodePositions[nodeNumber, 1] - halfWindowSize[1] - 1), int(nodePositions[nodeNumber, 1] + halfWindowSize[1] + 1 + 1)),
#slice(int(nodePositions[nodeNumber, 2] - halfWindowSize[2] - 1), int(nodePositions[nodeNumber, 2] + halfWindowSize[2] + 1 + 1))) #slice(int(nodePositions[nodeNumber, 2] - halfWindowSize[2] - 1), int(nodePositions[nodeNumber, 2] + halfWindowSize[2] + 1 + 1)))
#imagette1 = im1[subVolSlice1].copy() #imagette1 = im1[subVolSlice1].copy()
startStopIm1 = [int(nodePositions[nodeNumber, 0] - halfWindowSize[0] - 1), int(nodePositions[nodeNumber, 0] + halfWindowSize[0] + 1 + 1), startStopIm1 = [int(nodePositions[nodeNumber, 0] - halfWindowSize[0] - m), int(nodePositions[nodeNumber, 0] + halfWindowSize[0] + 1 + m),
int(nodePositions[nodeNumber, 1] - halfWindowSize[1] - 1), int(nodePositions[nodeNumber, 1] + halfWindowSize[1] + 1 + 1), int(nodePositions[nodeNumber, 1] - halfWindowSize[1] - 1), int(nodePositions[nodeNumber, 1] + halfWindowSize[1] + 1 + 1),
int(nodePositions[nodeNumber, 2] - halfWindowSize[2] - 1), int(nodePositions[nodeNumber, 2] + halfWindowSize[2] + 1 + 1)] int(nodePositions[nodeNumber, 2] - halfWindowSize[2] - 1), int(nodePositions[nodeNumber, 2] + halfWindowSize[2] + 1 + 1)]
imagette1, imagette1mask = spam.helpers.slicePadded(im1, startStopIm1, createMask=True) imagette1, imagette1mask = spam.helpers.slicePadded(im1, startStopIm1, createMask=True)
...@@ -487,7 +491,7 @@ def registerOnGrid(im1, im2, nodePositions, halfWindowSize, PhiField=None, margi ...@@ -487,7 +491,7 @@ def registerOnGrid(im1, im2, nodePositions, halfWindowSize, PhiField=None, margi
#slice(int(nodePositions[nodeNumber, 2] - halfWindowSize[2] + nodeDisplacement[2] - margin[2] - 1), int(nodePositions[nodeNumber, 2] + halfWindowSize[2] + nodeDisplacement[2] + margin[2] + 1 + 1))) #slice(int(nodePositions[nodeNumber, 2] - halfWindowSize[2] + nodeDisplacement[2] - margin[2] - 1), int(nodePositions[nodeNumber, 2] + halfWindowSize[2] + nodeDisplacement[2] + margin[2] + 1 + 1)))
## Extract it ## Extract it
#imagette2 = im2[subVolSlice2].copy() #imagette2 = im2[subVolSlice2].copy()
startStopIm2 = [int(nodePositions[nodeNumber, 0] - halfWindowSize[0] + nodeDisplacement[0] - margin[0] - 1), int(nodePositions[nodeNumber, 0] + halfWindowSize[0] + nodeDisplacement[0] + margin[0] + 1 + 1), startStopIm2 = [int(nodePositions[nodeNumber, 0] - halfWindowSize[0] + nodeDisplacement[0] - margin[0] - m), int(nodePositions[nodeNumber, 0] + halfWindowSize[0] + nodeDisplacement[0] + margin[0] + m + 1),
int(nodePositions[nodeNumber, 1] - halfWindowSize[1] + nodeDisplacement[1] - margin[1] - 1), int(nodePositions[nodeNumber, 1] + halfWindowSize[1] + nodeDisplacement[1] + margin[1] + 1 + 1), int(nodePositions[nodeNumber, 1] - halfWindowSize[1] + nodeDisplacement[1] - margin[1] - 1), int(nodePositions[nodeNumber, 1] + halfWindowSize[1] + nodeDisplacement[1] + margin[1] + 1 + 1),
int(nodePositions[nodeNumber, 2] - halfWindowSize[2] + nodeDisplacement[2] - margin[2] - 1), int(nodePositions[nodeNumber, 2] + halfWindowSize[2] + nodeDisplacement[2] + margin[2] + 1 + 1)] int(nodePositions[nodeNumber, 2] - halfWindowSize[2] + nodeDisplacement[2] - margin[2] - 1), int(nodePositions[nodeNumber, 2] + halfWindowSize[2] + nodeDisplacement[2] + margin[2] + 1 + 1)]
imagette2 = spam.helpers.slicePadded(im2, startStopIm2, padValue=numpy.nan) imagette2 = spam.helpers.slicePadded(im2, startStopIm2, padValue=numpy.nan)
...@@ -589,7 +593,7 @@ def registerOnGrid(im1, im2, nodePositions, halfWindowSize, PhiField=None, margi ...@@ -589,7 +593,7 @@ def registerOnGrid(im1, im2, nodePositions, halfWindowSize, PhiField=None, margi
# Get the next node off the queue # Get the next node off the queue
nodeNumber = q.get() nodeNumber = q.get()
imagetteReturns = getImagettes(nodeNumber, im1, im2, PhiField, nodePositions, margin, halfWindowSize, greyThreshold, im1mask, minMaskVolume) imagetteReturns = getImagettes(nodeNumber, im1, im2, PhiField, nodePositions, margin, halfWindowSize, greyThreshold, im1mask, minMaskVolume, twoD)
if imagetteReturns['returnStatus'] == 2: if imagetteReturns['returnStatus'] == 2:
if mpi: if mpi:
......
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