Bugfixes for zeissimport and dataset with transformations (9e096e02) · Commits · GEPARD / GEPARD

dataset.py

+3 −3

Original line number	Diff line number	Diff line
		@@ -216,7 +216,7 @@ class DataSet(object):
		Ngrid = len(self.grid)

		width, height, rotationvalue = self.imagedim_df
		p0, p1 = self.maxdim[:2], self.maxdim[2:]
		p0, p1 = self.lastpos[:2], self.maxdim[2:]
		for i in range(Ngrid):
		print(f"Processing image {i+1} of {Ngrid}")
		names = []
		@@ -271,7 +271,7 @@ class DataSet(object):
		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()
		z0, z1 = self.zpositions[0], self.zpositions[-1]
		return zp/255.*(z1-z0) + z0

		def mapHeight(self, x, y):
		@@ -296,7 +296,7 @@ class DataSet(object):

		elif mode == 'bf':
		p0[0] -= self.signx*self.imagedim_bf[0]/2
		p0[1] += self.signy*self.imagedim_bf[1]/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:

zeissimporter.py

+16 −9

Original line number	Diff line number	Diff line
		@@ -164,7 +164,10 @@ class ZeissImporter(QtWidgets.QDialog):
		z0, zn = self.zrange.z0, self.zrange.zn
		if zn<z0:
		zn, z0 = z0, zn
		dataset.zpositions = np.linspace(z0, zn, N)-zpc[2]
		# zeiss z axis has large values at the surface and smaller for large particles
		# that is why we need to invert the zpositions: zimg black corresponds to zn
		# zimg white corresponds to z0
		dataset.zpositions = np.linspace(z0, zn, N)[::-1]-zpc[2]
		dataset.heightmap = np.zeros(3)
		dataset.signy = 1.
		zimg = cv2imread_fix(self.zmapimgname, cv2.IMREAD_GRAYSCALE)
		@@ -174,24 +177,28 @@ class ZeissImporter(QtWidgets.QDialog):

		pshift = self.ramanctrl.getRamanPositionShift()
		dataset.pshift = pshift
		pixelscale = self.region.width/zimg.shape[1]
		pixelscale = self.region.scalex*1.e6

		# use input image as single image aquired in one shot
		dataset.imagedim_df = (self.region.width, self.region.height, 0.0)
		dataset.imagedim_df = (zimg.shape[1]*pixelscale,
		zimg.shape[0]*pixelscale, 0.0)
		dataset.pixelscale_df = pixelscale

		dataset.imagedim_bf = (self.region.width, self.region.height, 0.0)
		dataset.imagedim_bf = (zimg.shape[1]*pixelscale,
		zimg.shape[0]*pixelscale, 0.0)
		dataset.pixelscale_bf = pixelscale
		print('scale:', pixelscale)
		print('dim df:', dataset.imagedim_df)
		print('dim bf:', dataset.imagedim_bf)

		dataset.coordinatetransform = T, pc

		# set image center as reference point in data set (use Zeiss coordinates)
		# set image center as reference point (assume just one tile)
		# in data set (use Zeiss coordinates)
		p0center = np.array([self.region.centerx, self.region.centery]) - zpc[:2]
		p0 = p0center-.5*np.array((self.region.width, self.region.height))
		p1 = p0center+.5*np.array((self.region.width, self.region.height))
		dataset.readin = False
		dataset.lastpos = p0
		dataset.maxdim = p0 + p1
		dataset.lastpos = p0center
		dataset.maxdim = p0center

		zmin, zmax = dataset.zpositions.min(), dataset.zpositions.max()
		blur = (blur)*(255.)

zeissxml.py

+14 −4

Original line number	Diff line number	Diff line
		@@ -39,13 +39,15 @@ class Region:
		def __init__(self):
		self.centerx, self.centery = None, None
		self.width, self.height = None, None
		self.scalex, self.scaley = None, None

		def __repr__(self):
		return str(self)

		def __str__(self):
		return f'Region center: {self.centerx, self.centery} µm\n' + \
		f'Region size: {self.width, self.height} µm'
		f'Region size: {self.width, self.height} µm\n' + \
		f'Scale: {self.scalex, self.scaley} µm/pixel'

		class ZRange:
		def __init__(self):
		@@ -65,6 +67,7 @@ class ZeissHandler(handler.ContentHandler):
		self.zrange = ZRange()
		self.intag = False
		self.subtag = ''
		self.scaledim = ''

		def characters(self, content):
		if self.intag:
		@@ -75,20 +78,27 @@ class ZeissHandler(handler.ContentHandler):
		self.markers.append(Marker(attrs['Id'], attrs['StageXPosition'],
		attrs['StageYPosition'],
		attrs['FocusPosition']))
		elif name == 'TileRegion' or name == 'ZStackSetup':
		elif name == 'TileRegion' or name == 'ZStackSetup' or name == 'Scaling':
		self.intag = True
		if self.intag:
		self.content = ''
		if name in ['First','Last','Interval']:
		if self.subtag == 'Items' and name == 'Distance':
		self.scaledim = attrs['Id']
		if name in ['First','Last','Interval','Items']:
		self.subtag = name

		def endElement(self, name):
		if name == 'TileRegion' or name == 'ZStackSetup':
		if name == 'TileRegion' or name == 'ZStackSetup' or name == 'Scaling':
		self.intag = False
		if self.intag and name == 'CenterPosition':
		self.region.centerx, self.region.centery = map(float, self.content.split(','))
		elif self.intag and name == 'ContourSize':
		self.region.width, self.region.height = map(float, self.content.split(','))
		elif self.intag and self.subtag == 'Items' and name == 'Value':
		if self.scaledim == 'X':
		self.region.scalex = float(self.content)
		elif self.scaledim == 'Y':
		self.region.scaley = float(self.content)
		elif self.intag and name == 'Value' and \
		self.subtag in ['First','Last','Interval']:
		attrmap = {'First':'z0','Last':'zn','Interval':'dz'}