def build_with_map(self, mapfile):
this_xplor = xplor_map.reader(mapfile)
self.np_on_grid = (this_xplor.gridding.n[0]-1 ) /2 ## this is the np_on_grid stored in xplor map
self.np_on_grid = int(self.np_on_grid)
self.raw_map = this_xplor.data
self.map = flex.double( this_xplor.data.size(), 0)
self.id = mapfile.split('.')[0]
this_rmax = this_xplor.unit_cell.parameters()[0]/2.0
if(self.rmax is not None and ( self.rmax != this_rmax ) ): # do the scaling
grid=build_3d_grid(self.np_on_grid, this_rmax)
self.nlm_coefs = get_moments_for_scaled_model( self.raw_map, self.np_on_grid, grid, self.nmax, this_rmax, self.rmax)
self.nlm_array = math.nlm_array(self.nmax)
self.nlm_array.load_coefs(self.nlm_array.nlm(), self.nlm_coefs )
else:
self.rmax = this_rmax
print self.rmax,"test"
threshold = flex.max( self.raw_map )/3.0
select = flex.bool( this_xplor.data.as_1d() >= threshold )
self.map.set_selected( select, 1)
self.ngp = self.map.size() # number of grid point in 3D box
self.all_indx = flex.int(range( self.ngp ))
self.molecule = self.all_indx.select( select )
self.grid_obj=math.sphere_grid(self.np_on_grid, self.nmax)
ss = self.grid_obj.construct_space_sum_via_list( self.molecule.as_1d(), self.map.as_1d() )
self.moment_obj = math.zernike_moments( self.grid_obj, self.nmax )
self.moment_obj.calc_moments( ss.as_1d() )
self.nlm_array = self.moment_obj.moments()
self.nlm_coefs = self.nlm_array.coefs()
def load_maps(self,
files): # take about 0.5s to load one map, not big deal
xplor_file = files[0]
this_xplor = xplor_map.reader(xplor_file)
self.raw_map = this_xplor.data.as_1d()
self.np_on_grid = int((this_xplor.gridding.n[0] - 1) / 2)
def load_maps(self, files): # take about 0.5s to load one map, not big deal
xplor_file = files[0]
this_xplor = xplor_map.reader(xplor_file)
self.raw_map = flex.double( this_xplor.data.size(), 0)
threshold = flex.max( this_xplor.data )/4.0
for ii in range( this_xplor.data.size() ):
if( this_xplor.data[ii] > threshold ):
self.raw_map[ii] = 1
self.np_on_grid = (this_xplor.gridding.n[0]-1 ) /2
for xplor_file in files[1:]:
this_xplor = xplor_map.reader(xplor_file)
threshold = flex.max( this_xplor.data )/4.0
for ii in range( this_xplor.data.size() ):
if( this_xplor.data[ii] > threshold ):
self.raw_map[ii] += 1
def load_maps(self,
files): # take about 0.5s to load one map, not big deal
xplor_file = files[0]
this_xplor = xplor_map.reader(xplor_file)
self.raw_map = this_xplor.data.as_1d()
#self.raw_map = flex.double( this_xplor.data.size(), 0)
#threshold = flex.max( this_xplor.data )/4.0
#for ii in range( this_xplor.data.size() ):
# if( this_xplor.data[ii] > threshold ):
# self.raw_map[ii] = 1
self.np_on_grid = int((this_xplor.gridding.n[0] - 1) / 2)