def load(self, fName, stackUnits=[1., 1., 1.]):
if fName:
fNames = glob.glob(os.path.join(fName, "*"))
self.fNames = [f for f in fNames if re.match(".*\.(tif|tiff)", f)]
if len(self.fNames) == 0:
raise Exception("folder %s seems to be empty" % fName)
else:
self.fNames.sort()
try:
_tmp = imgutils.read3dTiff(self.fNames[0])
_single_size = _tmp.shape
if len(_single_size) == 2:
_single_size = (1, ) + _single_size
if len(_single_size) != 3:
raise Exception("tiff stacks seem to be neither 2d nor 3d")
self.stackSize = (len(self.fNames), ) + _single_size
except Exception as e:
print(e)
self.fName = ""
raise Exception("couldnt open %s as TiffData" % self.fNames[0])
return
self.stackUnits = stackUnits
self.fName = fName
def load(self, N=None):
if N == None:
logger.debug("loading precomputed demodata")
self.data = imgutils.read3dTiff(
absPath("../data/mpi_logo_80.tif")).astype(np.float32)
N = 80
self.stackSize = (10, N, N, N)
self.fName = ""
self.nT = 10
self.stackUnits = (1, 1, 1)
else:
self.stackSize = (1, N, N, N)
self.fName = ""
self.nT = N
self.stackUnits = (1, 1, 1)
x = np.linspace(-1, 1, N)
Z, Y, X = np.meshgrid(x, x, x, indexing="ij")
R = np.sqrt(X**2 + Y**2 + Z**2)
R2 = np.sqrt((X - .4)**2 + (Y + .2)**2 + Z**2)
phi = np.arctan2(Z, Y)
theta = np.arctan2(X, np.sqrt(Y**2 + Z**2))
u = np.exp(-500 * (R - 1.)**2) * np.sum(
np.exp(-150 * (
-theta - t + .1 *
(t - np.pi / 2.) * np.exp(-np.sin(2 *
(phi + np.pi / 2.))))**2)
for t in np.linspace(-np.pi / 2., np.pi / 2., 10)) * (1 + Z)
u2 = np.exp(-7 * R2**2)
self.data = (10000 * (u + 2 * u2)).astype(np.float32)
def load(self, N=None):
if N == None:
logger.debug("loading precomputed demodata")
self.data = imgutils.read3dTiff(absPath("../data/mpi_logo_80.tif")).astype(np.float32)
N = 80
self.stackSize = (10, N, N, N)
self.fName = ""
self.nT = 10
self.stackUnits = (1, 1, 1)
else:
self.stackSize = (1, N, N, N)
self.fName = ""
self.nT = N
self.stackUnits = (1, 1, 1)
x = np.linspace(-1, 1, N)
Z, Y, X = np.meshgrid(x, x, x, indexing="ij")
R = np.sqrt(X ** 2 + Y ** 2 + Z ** 2)
R2 = np.sqrt((X - .4) ** 2 + (Y + .2) ** 2 + Z ** 2)
phi = np.arctan2(Z, Y)
theta = np.arctan2(X, np.sqrt(Y ** 2 + Z ** 2))
u = np.exp(-500 * (R - 1.) ** 2) * np.sum(np.exp(-150 * (-theta - t + .1 * (t - np.pi / 2.) *
np.exp(-np.sin(2 * (phi + np.pi / 2.)))) ** 2)
for t in np.linspace(-np.pi / 2., np.pi / 2., 10)) * (1 + Z)
u2 = np.exp(-7 * R2 ** 2)
self.data = (10000 * (u + 2 * u2)).astype(np.float32)
def load(self, fName, stackUnits=[1., 1., 1.]):
if fName:
try:
data = np.squeeze(imgutils.read3dTiff(fName))
if not data.ndim in [2, 3, 4]:
raise ValueError(
"in file %s: dada.ndim = %s (not 2, 3 or 4)" %
(fName, data.ndim))
if data.ndim == 2:
self.stackSize = (1, 1) + data.shape
data = data.copy().reshape(self.stackSize)
elif data.ndim == 3:
self.stackSize = (1, ) + data.shape
data = data.copy().reshape(self.stackSize)
else:
self.stackSize = data.shape
self.data = data
except Exception as e:
print(e)
self.fName = ""
raise Exception("couldnt open %s as TiffData (%s)" %
(fName, str(e)))
return
self.stackUnits = stackUnits
self.fName = fName
def load(self, fName, stackUnits=[1., 1., 1.]):
if fName:
fNames = glob.glob(os.path.join(fName, "*"))
self.fNames = [f for f in fNames if re.match(".*\.(tif|tiff)", f)]
if len(self.fNames) == 0:
raise Exception("folder %s seems to be empty" % fName)
else:
self.fNames.sort()
try:
_tmp = imgutils.read3dTiff(self.fNames[0])
_single_size = _tmp.shape
if len(_single_size) == 2:
_single_size = (1,) + _single_size
if len(_single_size) != 3:
raise Exception("tiff stacks seem to be neither 2d nor 3d")
self.stackSize = (len(self.fNames),) + _single_size
except Exception as e:
print(e)
self.fName = ""
raise Exception("couldnt open %s as TiffData" % self.fNames[0])
return
self.stackUnits = stackUnits
self.fName = fName
def load(self, fName, stackUnits=[1., 1., 1.]):
if fName:
try:
data = np.squeeze(imgutils.read3dTiff(fName))
if not data.ndim in [2, 3, 4]:
raise ValueError("in file %s: dada.ndim = %s (not 2, 3 or 4)" % (fName, data.ndim))
if data.ndim == 2:
self.stackSize = (1, 1) + data.shape
data = data.copy().reshape(self.stackSize)
elif data.ndim == 3:
self.stackSize = (1,) + data.shape
data = data.copy().reshape(self.stackSize)
else:
self.stackSize = data.shape
self.data = data
except Exception as e:
print(e)
self.fName = ""
raise Exception("couldnt open %s as TiffData (%s)" % (fName,str(e)))
return
self.stackUnits = stackUnits
self.fName = fName
def __getitem__(self, pos):
if len(self.fNames) > 0 and pos < len(self.fNames):
try:
data = np.squeeze(imgutils.read3dTiff(self.fNames[pos]))
data = data.reshape(self.stackSize[1:])
except Exception as e:
print(e)
return None
return data
def __getitem__(self, pos):
if len(self.fNames) > 0 and pos < len(self.fNames):
try:
data = np.squeeze(imgutils.read3dTiff(self.fNames[pos]))
data = data.reshape(self.stackSize[1:])
except Exception as e:
print(e)
return None
return data
def load(self, fNames, stackUnits=[1., 1., 1.]):
if fNames:
if len(self.fNames) == 0:
raise Exception("filelist %s seems to be empty" % fNames)
try:
_tmp = imgutils.read3dTiff(self.fNames[0])
_single_size = _tmp.shape
if len(_single_size) == 2:
_single_size = (1, ) + _single_size
if len(_single_size) != 3:
raise Exception("tiff stacks seem to be neither 2d nor 3d")
self.stackSize = (len(self.fNames), ) + _single_size
except Exception as e:
print(e)
raise Exception("couldnt open %s as TiffData" % self.fNames[0])
return
self.stackUnits = stackUnits
def load(self, fNames, stackUnits=[1., 1., 1.]):
if fNames:
if len(self.fNames) == 0:
raise Exception("filelist %s seems to be empty" % fNames)
try:
_tmp = imgutils.read3dTiff(self.fNames[0])
_single_size = _tmp.shape
if len(_single_size) == 2:
_single_size = (1,) + _single_size
if len(_single_size) != 3:
raise Exception("tiff stacks seem to be neither 2d nor 3d")
self.stackSize = (len(self.fNames),) + _single_size
except Exception as e:
print(e)
raise Exception("couldnt open %s as TiffData" % self.fNames[0])
return
self.stackUnits = stackUnits
def main():
parser = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description="""renders max projectios of 3d data
example usage:
Tif data: \t \tspim_render -i mydata.tif -o myoutput.png -t 0 0 -4 -u 1 1 4
Bscope data: \tspim_render -f bscope -i mydataFolder -o myoutput.png -t 0 0 -4 -u 1 1 4
""")
parser.add_argument("-f","--format",dest="format",metavar="format",
help = """format currently supported:
tif (default)
bscope """,
type=str,default = "tif", required = False)
parser.add_argument("-i","--input",dest="input",metavar="infile",
help = "name of the input file to render, currently only 3d Tiff is supported",
type=str,default = None, required = True)
parser.add_argument("-o","--output",dest="output",metavar="outfile",
help = "name of the output file, png extension is recommended",
type=str,default = "out.png")
parser.add_argument("-p","--pos",dest="pos",metavar="timepoint position",
help = "timepoint to render if format=='bscope' ",
type=int,default = 0)
parser.add_argument("-w","--width",dest="width",metavar="width",
help = "pixelwidth of the rendered output ",
type=int,default = 400)
parser.add_argument("-s","--scale",dest="scale",metavar="scale",
type=float,nargs=1 ,default = [1.])
parser.add_argument("-u","--units",dest="units",metavar="units",
type=float,nargs= 3 ,default = [1.,1.,5.])
parser.add_argument("-t","--translate",dest="translate",
type = float, nargs=3,default = [0,0,-4],
metavar=("x","y","z"))
parser.add_argument("-r","--rotation",dest="rotation", type =
float, nargs=4,default = [0,1,0,0],
metavar=("w","x","y","z"))
parser.add_argument("-R","--range",dest="range", type =
float, nargs=2,default = None,
help = "if --16bit is set, the range of the data values to consider, defaults to [min,max]",
metavar=("min","max"))
parser.add_argument("-O","--Orthoview",help="use parallel projection (default: perspective)",
dest="ortho",action="store_true")
parser.add_argument("--16bit",help="render into 16 bit png",
dest="is16Bit",action="store_true")
if len(sys.argv)==1:
parser.print_help()
return
args = parser.parse_args()
for k,v in six.iteritems(vars(args)):
print(k,v)
rend = VolumeRenderer((args.width,args.width))
if args.format=="tif":
data = read3dTiff(args.input)
elif args.format=="bscope":
data = fromSpimFolder(args.input,pos=args.pos,count=1)[0,...]
else:
raise ValueError("format %s not supported (should be tif/bscope)" %args.format)
rend.set_data(data)
rend.set_units(args.units)
M = mat4_scale(*(args.scale*3))
M = np.dot(mat4_rotation(*args.rotation),M)
M = np.dot(mat4_translate(*args.translate),M)
rend.set_modelView(M)
if args.ortho:
rend.set_projection(mat4_ortho(-1,1,-1,1,-1,1))
else:
rend.set_projection(mat4_perspective(60,1.,1,10))
out = rend.render()
# image is saved by scipy.misc.toimage(out,low,high,cmin,cmax)
# p' = p * high/cmax
if not args.is16Bit:
imsave(args.output,out)
# if not args.range:
# imsave(args.output,out)
# else:
# img = toimage(out, low = args.range[0], high = args.range[1])
# img.save(args.output)
else:
if not args.range:
print("min/max: ", np.amin(out), np.amax(out))
img = toimage(out, low = np.amin(out), high = np.amax(out),mode = "I")
else:
img = toimage(out, low = args.range[0], high = args.range[1], mode = "I")
img.save(args.output)