#
# You should have received a copy of the GNU General Public License along
# with this program (LICENSE.txt). If not, see <http://www.gnu.org/licenses/>
import sys
sys.path.append(scriptdir + '..')
from eidolon import ReprType, ImageSceneObject, extendImage
from TestUtils import generateTimeSphereImages
step = 0.1
dim = 50
# create an object and repr with a particular name
images = generateTimeSphereImages(step, dim)
obj = ImageSceneObject('Sphere', [], images)
mgr.addSceneObject(obj)
rep = obj.createRepr(ReprType._imgtimevolume)
mgr.addSceneObjectRepr(rep)
del obj
del rep
mgr.clearScene() # this should free up existing objects
# attempt to create an object and repr with the same name as the above, this will crash if the repr doesn't choose unique names for materials, textures, etc.
images = generateTimeSphereImages(step, dim)
obj = ImageSceneObject('Sphere', [], images)
mgr.addSceneObject(obj)
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program (LICENSE.txt). If not, see <http://www.gnu.org/licenses/>
import sys
sys.path.append(scriptdir+'..')
from eidolon import ReprType,ImageSceneObject,extendImage
from TestUtils import generateTimeSphereImages
step=0.1
dim=30
mx=2
my=3
mz=4
fillVal=3.0
images=generateTimeSphereImages(step,dim)
obj=ImageSceneObject('Sphere',[],images)
mgr.addSceneObject(obj)
obj1=extendImage(obj,'ext',mx,my,mz,fillVal)
mgr.addSceneObject(obj1)
rep=obj1.createRepr(ReprType._imgtimestack)
mgr.addSceneObjectRepr(rep)
mgr.setCameraSeeAll()
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Eidolon is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program (LICENSE.txt). If not, see <http://www.gnu.org/licenses/>
from eidolon import ImageSceneObject, generateSphereImageStack, ReprType, delayedcall
images = generateSphereImageStack(50, 50, 50)
obj = ImageSceneObject('Sphere', [], images)
mgr.addSceneObject(obj)
rep = obj.createRepr(ReprType._imgstack)
mgr.addSceneObjectRepr(rep)
mgr.setCameraSeeAll()
d1 = mgr.create2DView()
mgr.callThreadSafe(d1.setImageStackPosition, 25)
d2 = mgr.create2DView()
mgr.callThreadSafe(d2.setImageStackPosition, 25)
# wait for 1 second, remove the second 2d window and then add a third
def _loadFile(filename,
name,
position=None,
rot=None,
toffset=None,
interval=None,
task=None):
with f:
filename = Future.get(filename)
name = name or self.mgr.getUniqueObjName(
splitPathExt(filename)[1])
recfile = os.path.splitext(filename)[0]
if os.path.exists(recfile + '.rec'):
recfile = recfile + '.rec'
elif os.path.exists(recfile + '.REC'):
recfile = recfile + '.REC'
else:
raise IOError("Cannot find rec file '%s.rec'" % recfile)
geninfo, imginfo = parseParFile(filename) # read par file
rec = np.fromfile(recfile, np.uint8) # read rec file
# numorients=geninfo[genInfoFields.maxgrad[2]][0]
# numslices=geninfo[genInfoFields.maxloc[2]][0]
# numsteps=geninfo[genInfoFields.maxphase[2]][0]
# slicenum=imgInfoFields.slicenum[-1]
# trigger=imgInfoFields.trigger[-1]
# numslices=len(set(i[slicenum] for i in imginfo))
# # count the number of times the slice number decreases one slice to the next, this indicates how many times the slice index loops back
# numorients=1+sum(1 if imginfo[i][slicenum]>imginfo[i+1][slicenum] else 0 for i in range(len(imginfo)-1))
# # count the number of times the trigger time decreases one slice to the next, this indicates when the images transition between volumes
# numvols=1+sum(1 if imginfo[i][trigger]>imginfo[i+1][trigger] else 0 for i in range(len(imginfo)-1))/(numorients*numslices)
# if len(imginfo)!=(numvols*numorients*numslices*numsteps):
# raise IOError,'Mismatch between stated orient, slice, and step numbers and number of images (%r != %r*%r*%r*%r)'%(len(imginfo),numorients,numslices,numsteps,numvols)
# orientsize=len(imginfo)/numorients
datasize = 0
objs = []
rpos = 0
typemap = {
} # maps type ID to dict mapping dynamic ID to SharedImage lists
for imgi in imginfo: # sum up the sizes of each image to compare against the actual size of the rec file
w, h = imgi[imgInfoFields.reconres[-1]]
pixelsize = imgi[imgInfoFields.imgpix[
-1]] / 8 # convert from bits to bytes
datasize += w * h * pixelsize
if rec.shape[0] != datasize:
raise IOError(
'Rec file incorrect size, should be %i but is %i' %
(datasize, rec.shape[0]))
for imgi in imginfo:
dynamic = imgi[imgInfoFields.dynnum[-1]]
itype = imgi[imgInfoFields.imgtypemr[-1]]
dims = imgi[imgInfoFields.reconres[-1]]
trigger = imgi[imgInfoFields.trigger[-1]]
orientation = imgi[imgInfoFields.sliceori[-1]]
spacing = imgi[imgInfoFields.pixspace[-1]]
offcenter = imgi[imgInfoFields.imgoff[-1]]
angulation = imgi[imgInfoFields.imgang[-1]]
pixelsize = imgi[imgInfoFields.imgpix[-1]]
reslope = imgi[imgInfoFields.rescalesl[-1]]
intercept = imgi[imgInfoFields.rescalein[-1]]
if itype not in typemap:
typemap[itype] = dict()
if dynamic not in typemap[itype]:
typemap[itype][dynamic] = []
images = typemap[itype][dynamic]
dtype = np.dtype('uint' + str(pixelsize))
pos, rot = getTransformFromInfo(offcenter,
angulation, orientation,
vec3(*spacing),
vec3(*dims))
imgsize = dims[0] * dims[1] * dtype.itemsize
arr = rec[rpos:rpos + imgsize].view(dtype).reshape(dims)
rpos += imgsize
if scalemethod in ('dv', 'DV'):
arr = (arr.astype(float) *
reslope) + intercept # DV scaling method
simg = SharedImage(recfile, pos, rot, dims, spacing,
trigger)
simg.allocateImg('%s_t%i_d%i_img%i' %
(name, itype, dynamic, len(images)))
#simg.setArrayImg(arr)
simg.setMinMaxValues(arr.min(), arr.max())
np.asarray(simg.img)[:, :] = arr
images.append(simg)
for itype in typemap:
for dynamic, images in typemap[itype].items():
vname = '%s_t%i_d%i' % (name, itype, dynamic)
source = {
'geninfo': geninfo,
'imginfo': imginfo,
'filename': filename,
'scalemethod': scalemethod,
'loadorder': len(objs)
}
obj = ImageSceneObject(vname, source, images, self)
objs.append(obj)
# for numo in range(numorients):
# orientimgs=imginfo[numo*orientsize:(numo+1)*orientsize]
#
# for numv in range(numvols):
# volsimgs=[img for i,img in enumerate(orientimgs) if i%numvols==numv]
# images=[]
# for imgi in volsimgs:
# vname='%s_o%i_v%i'%(name,numo,numv)
# dims=imgi[imgInfoFields.reconres[-1]]
# trigger=imgi[imgInfoFields.trigger[-1]]
# orientation=imgi[imgInfoFields.sliceori[-1]]
# spacing=imgi[imgInfoFields.pixspace[-1]]
# offcenter=imgi[imgInfoFields.imgoff[-1]]
# angulation=imgi[imgInfoFields.imgang[-1]]
# pixelsize=imgi[imgInfoFields.imgpix[-1]]
#
# reslope=imgi[imgInfoFields.rescalesl[-1]]
# intercept=imgi[imgInfoFields.rescalein[-1]]
#
# dtype=np.dtype('uint'+str(pixelsize))
#
# pos,rot=self._getTransformFromInfo(offcenter,angulation,orientation,vec3(*spacing),vec3(*dims))
#
# imgsize=dims[0]*dims[1]*dtype.itemsize
# arr=rec[rpos:rpos+imgsize].view(dtype).reshape(dims)
# rpos+=imgsize
#
# if scalemethod in ('dv','DV'):
# arr=(arr.astype(float)*reslope)+intercept # DV scaling method
#
# simg=SharedImage(recfile,pos,rot,dims,spacing,trigger)
# simg.allocateImg('%s_img%i'%(vname,len(images)))
# simg.setArrayImg(arr)
# images.append(simg)
#
# obj=ImageSceneObject(vname,{'geninfo':geninfo,'imginfo':imginfo,'filename':filename},images,self)
# objs.append(obj)
assert rpos == rec.shape[0], '%i != %i' % (rpos, rec.shape[0])
f.setObject(objs)