def __init__(self, data_xyz, data_j, shape=[10,10,2.5], title='',
rad_scale=1):
self.data_xyz = np.array(data_xyz)
self.data_j = np.array(data_j)
self.M = self.data_xyz.shape[0]
self.shape = shape # um
self.xlabel = utilmpl.shape2xlabel(self.shape)
self.title = title
self.rad_scale = rad_scale
def __init__(self, data_xyz, data_ijk, shape=[10,10,4], vmin=0, vmax=None, xlabel='', title='', invert=True,
rad_scale=1.0, skip_n=1):
self.data_xyz = data_xyz
self.data_ijk = data_ijk
self.shape = shape
self.xlabel = utilmpl.shape2xlabel(self.shape)
self.title = title
# Setup renderer
self.ren, self.renWin, self.iren = utilvtk.setup_render()
self.rad_scale = rad_scale*np.min(self.shape)/50
def __init__(self, data, vox_dims=[.1,.1,.1], N=2**10, title='',
skip_n=1, rad_scale=1, threshold=0):
self.data = data
self.npx = np.array(self.data.shape[0:3])
self.vox_dims = vox_dims # um
self.N = N
self.shape = np.array(data.shape[0:3])*np.array(vox_dims)
self.xlabel = utilmpl.shape2xlabel(self.shape)
self.title = title
self.skip_n = skip_n
self.rad_scale = rad_scale
self.threshold = threshold
# Calculate dimensions
self.lmax, mm = utilsh.j2lm(self.data.shape[-1] - 1)
self.J = utilsh.maxl2maxj(self.lmax)
def from_tiff(self, filename):
log.info('Reading '+filename)
with tifffile.TiffFile(filename) as tf:
# Read data
self.data = np.ascontiguousarray(np.moveaxis(tf.asarray(), [0, 1, 2, 3], [2, 3, 1, 0]))
# Read vox_dims from metadata
xx = tf.pages[0].tags['XResolution'].value
self.vox_dims[0] = xx[1]/xx[0]
yy = tf.pages[0].tags['YResolution'].value
self.vox_dims[1] = yy[1]/yy[0]
self.vox_dims[2] = tf.imagej_metadata['spacing']
self.npx = np.array(self.data.shape[0:3])
self.shape = np.array(self.npx)*np.array(self.vox_dims)
self.xlabel = utilmpl.shape2xlabel(self.shape)
self.lmax, mm = utilsh.j2lm(self.data.shape[-1] - 1)
self.J = utilsh.maxl2maxj(self.lmax)
def __init__(self, data_xyz, data_J, shape=[10,10,4], N=2**12, title=''):
self.data_xyz = np.array(data_xyz)
self.data_J = np.array(data_J)
self.M = self.data_xyz.shape[0]
self.N = N
self.shape = shape # um
self.xlabel = utilmpl.shape2xlabel(self.shape)
self.title = title
# Calculate dimensions
self.lmax, mm = utilsh.j2lm(self.data_J.shape[-1] - 1)
self.J = utilsh.maxl2maxj(self.lmax)
# Fill the rest of the last l band with zeros
if self.data_J.shape[-1] != self.J:
temp = np.zeros(self.J)
temp[:self.data_J.shape[-1]] = np.array(self.data_J)
self.data_J = temp
# Calc points for spherical plotting
self.xyz = utilsh.fibonacci_sphere(N, xyz=True)
self.B = utilsh.calcB(self.N, self.J)
def __init__(self,
data,
vox_dims=[1, 1, 1],
vmin=0,
vmax=None,
xlabel='',
title='',
invert=True):
self.data = data
self.shape = data.shape * np.array(vox_dims)
self.vox_dims = np.array(vox_dims)
self.invert = invert
self.xlabel = utilmpl.shape2xlabel(self.shape)
self.title = title
self.vmin = vmin
if vmax is None:
self.vmax = np.max(data)
else:
self.vmax = vnmax
# Setup renderer
self.ren, self.renWin, self.iren = utilvtk.setup_render()