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Commit f1fe95fd authored by Lars Bittrich's avatar Lars Bittrich
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tranformation fix to separate the previous implicit image orientation in pixel sign values

parent 10e10e12
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Showing with 681 additions and 652 deletions
analysis/database.py
View file @ f1fe95fd
......@@ -44,7 +44,7 @@ class DataBaseWindow(QtWidgets.QMainWindow):
self.path = os.path.join(Path.home(), 'gepard', 'databases')
self.importPath = self.path
if not os.path.exists(self.path):
os.mkdir(self.path)
os.makedirs(self.path)
self.activeDatabase = None
self.activeSpectrum = None
self.activeSpectrumName = None
......
dataset.py
View file @ f1fe95fd
......@@ -124,6 +124,9 @@ class DataSet(object):
self.zpositions = [] # z-positions for optical scan
self.heightmap = None
self.zvalimg = None
self.coordinatetransform = None # if imported form extern source coordinate system may be rotated
self.signx = 1.
self.signy = -1.
# parameters specifically for raman scan
self.pshift = None # shift of raman scan position relative to image center
......@@ -260,7 +263,14 @@ class DataSet(object):
def getZval(self, pixelpos):
assert self.zvalimg is not None
zp = self.zvalimg[round(pixelpos[1]), round(pixelpos[0])]
i, j = int(round(pixelpos[1])), int(round(pixelpos[0]))
if i>=self.zvalimg.shape[0]:
print('error in getZval:', self.zvalimg.shape, i, j)
i = self.zvalimg.shape[0]-1
if j>=self.zvalimg.shape[1]:
print('error in getZval:', self.zvalimg.shape, i, j)
j = self.zvalimg.shape[1]-1
zp = self.zvalimg[i,j]
z0, z1 = self.zpositions.min(), self.zpositions.max()
return zp/255.*(z1-z0) + z0
......@@ -274,44 +284,59 @@ class DataSet(object):
assert not self.readin
p0 = copy(self.lastpos)
if self.coordinatetransform is not None:
z = 0. if len(p)<3 else p[2]
T, pc = self.coordinatetransform
p = (np.dot(np.array([p[0], p[1], z])-pc, T.T))
if mode == 'df':
p0[0] -= self.imagedim_df[0]/2
p0[1] += self.imagedim_df[1]/2
return (p[0] - p0[0])/self.pixelscale_df, (p0[1] - p[1])/self.pixelscale_df
p0[0] -= self.signx*self.imagedim_df[0]/2
p0[1] -= self.signy*self.imagedim_df[1]/2
x, y = self.signx*(p[0] - p0[0])/self.pixelscale_df, self.signy*(p[1] - p0[1])/self.pixelscale_df
elif mode == 'bf':
p0[0] -= self.imagedim_bf[0]/2
p0[1] += self.imagedim_bf[1]/2
return (p[0] - p0[0])/self.pixelscale_bf, (p0[1] - p[1])/self.pixelscale_bf
p0[0] -= self.signx*self.imagedim_bf[0]/2
p0[1] += self.signy*self.imagedim_bf[1]/2
x, y = self.signx*(p[0] - p0[0])/self.pixelscale_bf, self.signy*(p[1] - p0[1])/self.pixelscale_bf
else:
print('mapToPixelMode not understood')
return
raise ValueError(f'mapToPixel mode: {mode} not understood')
return x, y
def mapToLength(self, pixelpos, mode='df', force=False):
def mapToLength(self, pixelpos, mode='df', force=False, returnz=False):
if not force:
assert not self.readin
p0 = copy(self.lastpos)
p0[0] += self.coordOffset[0]
p0[1] += self.coordOffset[1]
if mode == 'df':
p0[0] -= self.imagedim_df[0]/2
p0[1] += self.imagedim_df[1]/2
return (pixelpos[0]*self.pixelscale_df + p0[0]), (p0[1] - pixelpos[1]*self.pixelscale_df)
p0[0] -= self.signx*self.imagedim_df[0]/2
p0[1] -= self.signy*self.imagedim_df[1]/2
x, y = (self.signx*pixelpos[0]*self.pixelscale_df + p0[0]), (p0[1] + self.signy*pixelpos[1]*self.pixelscale_df)
elif mode == 'bf':
p0[0] -= self.imagedim_bf[0]/2
p0[1] += self.imagedim_bf[1]/2
return (pixelpos[0]*self.pixelscale_bf + p0[0]), (p0[1] - pixelpos[1]*self.pixelscale_bf)
p0[0] -= self.signx*self.imagedim_bf[0]/2
p0[1] -= self.signy*self.imagedim_bf[1]/2
x, y = (self.signx*pixelpos[0]*self.pixelscale_bf + p0[0]), (p0[1] + self.signy*pixelpos[1]*self.pixelscale_bf)
else:
raise ValueError(f'mapToLength mode: {mode} not understood')
def mapToLengthRaman(self, pixelpos, microscopeMode='df', noz=False):
p0x, p0y = self.mapToLength(pixelpos, mode = microscopeMode)
x, y = p0x + self.pshift[0], p0y + self.pshift[1]
z = None
if not noz:
if (returnz and self.zvalimg is not None) or self.coordinatetransform is not None:
z = self.mapHeight(x, y)
z += self.getZval(pixelpos)
if self.coordinatetransform is not None:
T, pc = self.coordinatetransform
x, y, z = (np.dot(np.array([x,y,z]), T) + pc)
if returnz:
return x, y, z
return x, y
def mapToLengthRaman(self, pixelpos, microscopeMode='df', noz=False):
p0x, p0y, z = self.mapToLength(pixelpos, mode=microscopeMode, returnz=True)
x, y = p0x + self.pshift[0], p0y + self.pshift[1]
return x, y, z
def newProject(self, fname):
......
helperfunctions.py
View file @ f1fe95fd
......@@ -23,7 +23,16 @@ import numpy as np
import cv2
import os
try:
from skimage.io import imread as skimread
from skimage.io import imsave as skimsave
except ImportError:
skimread = None
skimsave = None
def cv2imread_fix(fname, flags=cv2.IMREAD_COLOR):
if skimread is not None:
return skimread(fname, as_gray=(flags==cv2.IMREAD_GRAYSCALE))
with open(fname, "rb") as fp:
cont = fp.read()
img = cv2.imdecode(np.fromstring(cont, dtype=np.uint8), flags)
......@@ -31,6 +40,8 @@ def cv2imread_fix(fname, flags=cv2.IMREAD_COLOR):
return None
def cv2imwrite_fix(fname, img, params=None):
if skimsave is not None:
skimsave(fname, img)
pathname, ext = os.path.splitext(fname)
if params is None:
ret, data = cv2.imencode(ext, img)
......
zeissimporter.py
View file @ f1fe95fd
......@@ -59,6 +59,10 @@ class ZeissImporter(QtWidgets.QDialog):
self.pexit.released.connect(self.reject)
self.pconvert.setEnabled(False)
self.xinvert = QtWidgets.QCheckBox('Invert x-axis')
self.yinvert = QtWidgets.QCheckBox('Invert y-axis')
self.zinvert = QtWidgets.QCheckBox('Invert z-axis')
btnLayout = QtWidgets.QHBoxLayout()
btnLayout.addStretch()
btnLayout.addWidget(self.pconvert)
......@@ -77,22 +81,30 @@ class ZeissImporter(QtWidgets.QDialog):
vbox.addWidget(pointgroup)
vbox.addLayout(blurlayout)
vbox.addWidget(self.xinvert)
vbox.addWidget(self.yinvert)
vbox.addWidget(self.zinvert)
vbox.addLayout(btnLayout)
self.setLayout(vbox)
def readImportData(self, fname):
path = os.path.split(fname)[0]
self.zmapimgname = os.path.join(path, '3D.tif')
self.edfimgname = os.path.join(path, 'EDF.tif')
xmlname = os.path.join(path, '3D.tif_metadata.xml')
self.edfimgname, self.zmapimgname, xmlname = '', '', ''
for name in os.listdir(path):
if name.lower().endswith('_meta.xml'):
xmlname = os.path.join(path, name)
elif name.lower().endswith('_c1.tif'):
self.edfimgname = os.path.join(path, name)
elif name.lower().endswith('_c2.tif'):
self.zmapimgname = os.path.join(path, name)
errmsges = []
if not os.path.exists(self.zmapimgname):
errmsges.append('Depth map image not found: 3D.tif')
errmsges.append('Depth map image not found: NAME_c2.tif')
if not os.path.exists(self.edfimgname):
errmsges.append('EDF image not found: EDF.tif')
errmsges.append('EDF image not found: NAME_c1.tif')
if not os.path.exists(xmlname):
errmsges.append('XML metadata not found: 3D.tif_metadata.xml')
errmsges.append('XML metadata not found: NAME_meta.xml')
else:
parser = make_parser()
z = ZeissHandler()
......@@ -108,7 +120,7 @@ class ZeissImporter(QtWidgets.QDialog):
errmsges.append('ZStack information missing or incomplete!')
if len(errmsges)>0:
QtWidgets.QMessageBox.error(self, 'Error!',
QtWidgets.QMessageBox.critical(self, 'Error!',
'\n'.join(errmsges),
QtWidgets.QMessageBox.Ok,
QtWidgets.QMessageBox.Ok)
......@@ -117,6 +129,9 @@ class ZeissImporter(QtWidgets.QDialog):
self.region = z.region
self.zrange = z.zrange
self.markers = z.markers
print(self.region)
print(self.zrange)
print(self.markers, flush=True)
return True
@QtCore.pyqtSlot(float, float, float)
......@@ -127,32 +142,33 @@ class ZeissImporter(QtWidgets.QDialog):
@QtCore.pyqtSlot()
def convert(self):
T, pc, zpc, accept = self.getTransform()
if accept:
fname = QtWidgets.QFileDialog.getSaveFileName(self,
'Create New GEPARD Project', defaultPath, '*.pkl')[0]
if fname=='':
return
dataset = DataSet(fname, newProject=True)
T, pc, zpc = self.getTransform()
imgshape, warp_mat = self.convertZimg(dataset, T, pc, zpc)
self.convertImage(dataset, warp_mat)
self.convertZimg(dataset, T, pc, zpc)
self.convertImage(dataset)
dataset.save()
self.gepardname = dataset.fname
self.accept()
def convertImage(self, dataset, warp_mat):
def convertImage(self, dataset):
img = cv2imread_fix(self.edfimgname)
img = cv2.warpAffine(img, warp_mat, img.shape[:2][::-1])
cv2imwrite_fix(dataset.getImageName(), img)
def convertZimg(self, dataset, T, pc, zpc):
N = int(round((self.zrange.zn-self.zrange.z0)/self.zrange.dz))
dataset.zpositions = np.linspace(self.zrange.z0,
self.zrange.zn, N)-zpc[2]+pc[2]
N = int(round(abs(self.zrange.zn-self.zrange.z0)/self.zrange.dz))
z0, zn = self.zrange.z0, self.zrange.zn
if zn<z0:
zn, z0 = z0, zn
dataset.zpositions = np.linspace(z0, zn, N)-zpc[2]
dataset.heightmap = np.zeros(3)
dataset.signy = 1.
zimg = cv2imread_fix(self.zmapimgname, cv2.IMREAD_GRAYSCALE)
zmdist = zimg.mean()
zm = zmdist/255.*(self.zrange.zn-self.zrange.z0) + self.zrange.z0
print("zimg shape:", zimg.shape, flush=True)
radius = self.blurspinbox.value()
blur = cv2.GaussianBlur(zimg, (radius, radius), 0)
......@@ -167,53 +183,32 @@ class ZeissImporter(QtWidgets.QDialog):
dataset.imagedim_bf = (self.region.width, self.region.height, 0.0)
dataset.pixelscale_bf = pixelscale
# set image center as reference point in data set (transform from Zeiss)
p0 = np.dot((np.array([self.region.centerx,
self.region.centery,zm])-zpc),T)[:2] + pc[:2]
dataset.coordinatetransform = T, pc
# set image center as reference point in data set (use Zeiss coordinates)
p0 = np.array([self.region.centerx, self.region.centery]) - zpc[:2]
dataset.readin = False
dataset.lastpos = p0
dataset.maxdim = p0 + p0
# pixel triangle for coordinate warping transformation
srcTri = np.array( [[0, 0], [zimg.shape[1] - 1, 0],
[0, zimg.shape[0] - 1]] ).astype(np.float32)
# upper left point (0,0) in Zeiss coordinates:
z0 = np.array([self.region.centerx - self.region.width/2,
self.region.centery + self.region.height/2])
# transform pixel data to Zeiss coordinates
dstTri = np.array([[p[0]*pixelscale + z0[0],
z0[1] - p[1]*pixelscale, zm] for p in srcTri]).astype(np.double)-zpc
# transform to Raman coordinates
dstTri = np.dot(dstTri,T) + pc[np.newaxis,:]
# tilt blur image based on transformend z and adapt zpositions
x = np.linspace(0,1,blur.shape[1])
y = np.linspace(0,1,blur.shape[0])
x, y = np.meshgrid(x,y)
zmap = x*(dstTri[1,2]-dstTri[0,2]) + y*(dstTri[2,2]-dstTri[0,2]) + \
(zimg * ((self.zrange.zn-self.zrange.z0)/255.) - \
zmdist*((self.zrange.zn-self.zrange.z0)/255.))
zmin, zmax = zmap.min(), zmap.max()
dataset.zpositions = np.array([zmap.min(), zmap.max()])
blur = (zmap-zmin)*(255./(zmax-zmin))
zmin, zmax = dataset.zpositions.min(), dataset.zpositions.max()
blur = (blur)*(255.)
blur[blur>255.] = 255.
blur[np.isnan(blur)] = 0.
blur = np.uint8(blur)
# transform triangle back to pixel
dstTri = np.array([dataset.mapToPixel(p[:2]) for p in dstTri]).astype(np.float32)
warp_mat = cv2.getAffineTransform(srcTri, dstTri)
blur = cv2.warpAffine(blur, warp_mat, zimg.shape[::-1])
zimgname = dataset.getZvalImageName()
cv2imwrite_fix(zimgname, blur)
return zimg.shape, warp_mat
dataset.zvalimg = "saved"
def getTransform(self):
points = self.points.getPoints()
pshift = self.ramanctrl.getRamanPositionShift()
points[:,0] -= pshift[0]
points[:,1] -= pshift[1]
Parity = np.mat(np.diag([-1. if self.xinvert.isChecked() else 1.,
-1. if self.yinvert.isChecked() else 1.,
-1. if self.zinvert.isChecked() else 1.]))
zpoints = np.array([m.getPos() for m in self.markers], dtype=np.double)
pc = points.mean(axis=0)
zpc = zpoints.mean(axis=0)
......@@ -233,11 +228,10 @@ class ZeissImporter(QtWidgets.QDialog):
# [-45°,45°] for all permutation of markers
permbest = None
pointsbest = None
for perm in permutations(range(points.shape[0])):
ppoints = points[perm,:]
ppoints = points[:,:].copy()
def err(angles_shift):
T = getRotMat(angles_shift[:3]).T.A
T = (getRotMat(angles_shift[:3]).T*Parity).A
return (np.dot(zpoints, T) - angles_shift[np.newaxis,3:] \
- ppoints).ravel()
......@@ -246,25 +240,24 @@ class ZeissImporter(QtWidgets.QDialog):
bounds=(np.array([-np.pi/4]*3+[-np.inf]*3),
np.array([np.pi/4]*3+[np.inf]*3)),
method='dogbox')
if permbest is None or \
permbest.cost>opt.cost:
print("Current best permutation:", perm, flush=True)
permbest = opt
pointsbest = ppoints
optangles = permbest.x[:3]
shift = permbest.x[3:]
T = getRotMat(optangles).T.A
T = (getRotMat(optangles).T*Parity).A
e = (np.dot(zpoints, T)-shift[np.newaxis,:]-pointsbest)
print("Transformation angles:", optangles, flush=True)
print("Transformation shift:", shift, flush=True)
print("Transformation err:", e, flush=True)
d = np.linalg.norm(e, axis=1)
accept = True
if np.any(d>1.):
QtWidgets.QMessageBox.warning(self, 'Warning!',
ret = QtWidgets.QMessageBox.warning(self, 'Warning!',
f'Transformation residuals are large:{d}',
QtWidgets.QMessageBox.Ok,
QtWidgets.QMessageBox.Ok|QtWidgets.QMessageBox.Cancel,
QtWidgets.QMessageBox.Ok)
return T, pc-shift, zpc
if ret==QtWidgets.QMessageBox.Cancel:
accept = False
return T, pc-shift, zpc, accept
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