def load_grid(fname, prefix='aa', ramp='jet'):
cmd.volume_ramp_new('ramp_jet', [
0.00,
0.00,
0.00,
1.00,
0.00,
25.00,
0.06,
0.93,
1.00,
0.05,
50.00,
0.49,
0.51,
1.00,
0.15,
75.00,
1.00,
1.00,
0.00,
0.23,
90.00,
0.80,
0.18,
1.00,
0.48,
100.00,
0.98,
0.01,
1.00,
1.00,
])
cmd.volume_ramp_new('ramp_delta', [
-1.0, 1.00, 0.00, 0.00, 0.00, -0.4, 1.00, 1.00, 0.00, 1.0, -0.2, 1.00,
0.00, 0.00, 0.00, 0.2, 0.00, 0.00, 1.00, 0.00, 0.4, 0.00, 1.00, 1.00,
1.0, 1.0, 0.00, 0.00, 1.00, 0.00
])
F = h5py.File(fname, 'r')
grid = F['step'][()]
origin = F['origin'][()]
NUCS = set(F.keys())
protected = set(['origin', 'step', 'atypes'])
NUCS -= protected
for i in NUCS:
data = F[i][()]
b = Brick.from_numpy(data, grid, origin)
bname = prefix + '_' + i
cmd.load_brick(b, bname)
volname = bname + '_volume'
cmd.volume(volname, bname)
cmd.volume_color(volname, 'ramp_jet')
def test(self):
try:
import numpy
except ImportError:
self.skip('requires numpy')
from chempy.brick import Brick
spacing = (.5, .5, .5)
origin = (3., 4., 5.)
shape = (10, 10, 10)
range_ = [a * (b - 1) for (a, b) in zip (spacing, shape)]
data = numpy.zeros(shape, float)
brick = Brick.from_numpy(data, spacing, origin)
self.assertArrayEqual(brick.range, range_)
cmd.load_brick(brick, 'map')
extent = cmd.get_extent('map')
self.assertArrayEqual(extent, [origin, cpv.add(origin, range_)])
# ===============================
# brick creation
from chempy.brick import Brick
brik = Brick()
brik.setup_from_min_max(
[0.0,0.0,0.0],
[2.0,2.0,2.0],
[0.2,0.2,0.2])
# ===============================
# brick data
import math
for x in range(11):
for y in range(11):
for z in range(11):
mx=1.5*(x-5)
my=2*(y-5)
mz=3*(z-5)
brik.lvl[x,y,z]=1/math.exp(math.sqrt(mx*mx+my*my+mz*mz)/10.0)
# ===============================
# easy pickling code
def load_nrrd(filename, prefix='channel', channel='', _self=cmd):
'''
DESCRIPTION
Load maps in NRRD file format.
Spec:
http://teem.sourceforge.net/nrrd/format.html
Example files:
http://www.cs.utah.edu/~jmk/simian/download.htm
'''
import numpy
import shlex
from chempy.brick import Brick
handle = open(filename, 'rb')
magic = handle.readline()
assert magic.startswith('NRRD')
header = {}
while True:
line = handle.readline()
if not line.strip():
break
if line.startswith('#'):
continue
key, value = line.split(':')
header[key] = value.strip()
assert header['encoding'] == 'raw'
endian = '>' if header.get('endian') == 'big' else '<'
dtype = {
'signed char': 'i1',
'int8': 'i1',
'int8_t': 'i1',
'uchar': 'u1',
'unsigned char': 'u1',
'uint8': 'u1',
'uint8_t': 'u1',
'float': 'f4',
'double': 'f8',
}[header['type']]
data = numpy.fromfile(handle, endian + dtype)
handle.close()
sizes = [int(i) for i in header['sizes'].split()]
grid = [float(i) for i in header.get('spacings', '0 1 1 1').split()[1:]]
channels = shlex.split(header.get('labels', 'abcdefg'))[0]
assert len(sizes) == 4
sizes = tuple(reversed(sizes))
grid = tuple(reversed(grid))
data = data.reshape(sizes)
for i in range(sizes[-1]):
ch = channels[i]
name = prefix
if not channel:
name += '_' + ch
elif channel != ch:
continue
stack = data[..., i].astype('f4')
# normalize
stack -= stack.mean()
stack /= stack.std()
brick = Brick.from_numpy(stack, grid)
_self.load_brick(brick, name)
def load_grid(fname, prefix='aa', ramp='jet'):
cmd.volume_ramp_new('ramp_DA', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
1.00,
0.77,
0.77,
0.02,
50.00,
1.00,
0.54,
0.54,
0.06,
75.00,
1.00,
0.38,
0.38,
0.18,
90.00,
0.93,
0.00,
0.00,
0.60,
100.00,
0.70,
0.00,
0.00,
1.00,
])
cmd.volume_ramp_new('ramp_DG', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
0.77,
0.77,
1.00,
0.02,
50.00,
0.54,
0.54,
1.00,
0.06,
75.00,
0.38,
0.38,
1.00,
0.18,
90.00,
0.00,
0.00,
0.93,
0.60,
100.00,
0.00,
0.00,
0.70,
1.00,
])
cmd.volume_ramp_new('ramp_DC', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
0.64,
1.00,
0.61,
0.02,
50.00,
0.48,
1.00,
0.47,
0.06,
75.00,
0.26,
1.00,
0.28,
0.18,
90.00,
0.04,
0.85,
0.00,
0.44,
100.00,
0.00,
0.52,
0.06,
1.00,
])
cmd.volume_ramp_new('ramp_DT', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
1.00,
0.99,
0.55,
0.02,
50.00,
1.00,
0.98,
0.46,
0.06,
75.00,
1.00,
0.99,
0.37,
0.19,
90.00,
0.92,
0.92,
0.00,
0.39,
100.00,
0.76,
0.73,
0.00,
1.00,
])
cmd.volume_ramp_new('ramp_P', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
1.00,
0.95,
0.93,
0.02,
50.00,
1.00,
0.85,
0.69,
0.06,
75.00,
1.00,
0.78,
0.55,
0.19,
90.00,
1.00,
0.66,
0.30,
0.39,
100.00,
0.97,
0.50,
0.00,
1.00,
])
cmd.volume_ramp_new('ramp_jet', [
0.00,
0.00,
0.00,
1.00,
0.00,
25.00,
0.06,
0.93,
1.00,
0.05,
50.00,
0.49,
0.51,
1.00,
0.15,
75.00,
1.00,
1.00,
0.00,
0.23,
90.00,
0.80,
0.18,
1.00,
0.48,
100.00,
0.98,
0.01,
1.00,
1.00,
])
cmd.volume_ramp_new('ramp_delta', [
-1.0, 1.00, 0.00, 0.00, 0.00, -0.4, 1.00, 1.00, 0.00, 1.0, -0.2, 1.00,
0.00, 0.00, 0.00, 0.2, 0.00, 0.00, 1.00, 0.00, 0.4, 0.00, 1.00, 1.00,
1.0, 1.0, 0.00, 0.00, 1.00, 0.00
])
F = h5py.File(fname, 'r')
# load step along every axis
# step = np.array([1.0, 1.0, 1.0])
step = F['step'][()]
# load origin of grid
# origin = np.array([0.0, 0.0, 0.0])
origin = F['origin'][()]
NUCS = set(F.keys())
protected = set(['origin', 'step', 'atypes'])
NUCS -= protected
for i in NUCS:
# load data: 3D array
data = F[i][()]
# Create brick
b = Brick.from_numpy(data, step, origin)
bname = prefix + '_' + i
# load brick into pymol
cmd.load_brick(b, bname)
volname = bname + '_volume'
# assign ramp to the brick
cmd.volume(volname, bname)
if ramp == 'nuc':
cmd.volume_color(volname, 'ramp_' + i)
elif ramp == 'delta':
cmd.volume_color(volname, 'ramp_delta')
else:
cmd.volume_color(volname, 'ramp_jet')
def load_meta_grid(fname, prefix='meta'):
F = h5py.File(fname, 'r')
step = F['step'][()]
origin = F['origin'][()]
NUCS = set(F.keys())
protected = set(['origin', 'step', 'atypes'])
NUCS -= protected
for i in NUCS:
data = F[i][()]
b = Brick.from_numpy(data, step, origin)
bname = prefix + '_' + i
cmd.load_brick(b, bname)
volname = bname + '_volume'
d_min = np.min(data)
d_max = np.max(data)
v = np.linspace(d_min, d_max, 6)
cmd.volume(volname, bname)
print('ramp_%s' % i)
cmd.volume_ramp_new('ramp_grid', [
v[0],
0.00,
0.00,
1.00,
0.70,
v[1],
0.06,
0.93,
1.00,
0.50,
v[2],
0.49,
0.51,
1.00,
0.30,
v[3],
1.00,
1.00,
0.00,
0.10,
v[4],
0.80,
0.18,
1.00,
0.05,
v[5],
0.98,
0.01,
1.00,
0.00,
])
cmd.volume_color(volname, 'ramp_grid')
# ===============================
# brick creation
from chempy.brick import Brick
brik = Brick()
brik.setup_from_min_max([0.0, 0.0, 0.0], [2.0, 2.0, 2.0], [0.2, 0.2, 0.2])
# ===============================
# brick data
import math
for x in range(11):
for y in range(11):
for z in range(11):
mx = 1.5 * (x - 5)
my = 2 * (y - 5)
mz = 3 * (z - 5)
brik.lvl[x, y, z] = 1 / math.exp(
math.sqrt(mx * mx + my * my + mz * mz) / 10.0)
# ===============================
# easy pickling code
#from chempy import io
#io.pkl.toFile(brik,"brick.pkb")
#brik = io.pkl.fromFile("brick.pkb")
def load_img_stack(pattern,
name='',
grid=1.0,
channel=0,
normalize=1,
extent=None,
quiet=1,
_self=cmd):
'''
DESCRIPTION
Load a stack of images as a map
ARGUMENTS
pattern = str: image filename or pattern
name = str: map object name to create
grid = float: grid spacing in Angstrom {default: 1.0}
channel = int: color channel for RGB images {default: 0}
normalize = 0 or 1: normalize data {default: 1}
extent = 3-float: (a,b,c) edge lengths in Angstrom, overwrites "grid"
arguments if given {default: }
EXAMPLES
load_img_stack img*.tif, extent=(21.0, 14.5, 18.2)
'''
import glob
import numpy
from chempy.brick import Brick
try:
from PIL import Image
except ImportError:
import Image
channel, normalize, quiet = int(channel), int(normalize), int(quiet)
if not name:
name = _self.get_unused_name('map')
if isinstance(grid, str):
grid = _self.safe_eval(grid)
if not isinstance(grid, (tuple, list)):
grid = (grid, ) * 3
stack = []
size = None
filenames = glob.glob(_self.exp_path(pattern))
if not filenames:
raise CmdException('no such files')
for filename in sorted(filenames):
img = Image.open(filename)
if size is None:
size = img.size
for img in imgframeiter(img):
if img.size != size:
if not quiet:
print('Image size mismatch: %s != %s' % (img.size, size))
continue
a = numpy.reshape(img, (size[0], size[1], -1))
stack.append(a[..., channel])
stack = numpy.asfarray(stack)
stack = stack.swapaxes(0, 2)[:, ::-1, ::-1]
if min(stack.shape) < 2:
raise CmdException('insufficient grid dimensions: ' + str(stack.shape))
if normalize:
stack -= stack.mean()
stack /= stack.std()
if extent:
if isinstance(extent, str):
extent = _self.safe_eval(extent)
grid = [(float(e) / (s - 1)) for (e, s) in zip(extent, stack.shape)]
if not quiet:
print(' Setting grid = ' + str(grid))
brick = Brick.from_numpy(stack, grid)
_self.load_brick(brick, name)
def load_img_stack(pattern, name='', grid=1.0, channel=0, normalize=1,
extent=None, quiet=1, _self=cmd):
'''
DESCRIPTION
Load a stack of images as a map
ARGUMENTS
pattern = str: image filename or pattern
name = str: map object name to create
grid = float: grid spacing in Angstrom {default: 1.0}
channel = int: color channel for RGB images {default: 0}
normalize = 0 or 1: normalize data {default: 1}
extent = 3-float: (a,b,c) edge lengths in Angstrom, overwrites "grid"
arguments if given {default: }
EXAMPLES
load_img_stack img*.tif, extent=(21.0, 14.5, 18.2)
'''
import glob
import numpy
from chempy.brick import Brick
try:
from PIL import Image
except ImportError:
import Image
channel, normalize, quiet = int(channel), int(normalize), int(quiet)
if not name:
name = _self.get_unused_name('map')
if isinstance(grid, str):
grid = _self.safe_eval(grid)
if not isinstance(grid, (tuple, list)):
grid = (grid,) * 3
stack = []
size = None
filenames = glob.glob(_self.exp_path(pattern))
if not filenames:
raise CmdException('no such files')
for filename in sorted(filenames):
img = Image.open(filename)
if size is None:
size = img.size
for img in imgframeiter(img):
if img.size != size:
if not quiet:
print('Image size mismatch: %s != %s' % (img.size, size))
continue
a = numpy.reshape(img, (size[0], size[1], -1))
stack.append(a[..., channel])
stack = numpy.asfarray(stack)
stack = stack.swapaxes(0, 2)[:, ::-1, ::-1]
if min(stack.shape) < 2:
raise CmdException('insufficient grid dimensions: ' + str(stack.shape))
if normalize:
stack -= stack.mean()
stack /= stack.std()
if extent:
if isinstance(extent, str):
extent = _self.safe_eval(extent)
grid = [(float(e) / (s - 1)) for (e, s) in zip(extent, stack.shape)]
if not quiet:
print(' Setting grid = ' + str(grid))
brick = Brick.from_numpy(stack, grid)
_self.load_brick(brick, name)
def load_sites(fname, prefix='sites', ramp='jet', top=42):
cmd.volume_ramp_new('ramp_DA', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
1.00,
0.77,
0.77,
0.02,
50.00,
1.00,
0.54,
0.54,
0.06,
75.00,
1.00,
0.38,
0.38,
0.18,
90.00,
0.93,
0.00,
0.00,
0.60,
100.00,
0.70,
0.00,
0.00,
1.00,
])
cmd.volume_ramp_new('ramp_DG', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
0.77,
0.77,
1.00,
0.02,
50.00,
0.54,
0.54,
1.00,
0.06,
75.00,
0.38,
0.38,
1.00,
0.18,
90.00,
0.00,
0.00,
0.93,
0.60,
100.00,
0.00,
0.00,
0.70,
1.00,
])
cmd.volume_ramp_new('ramp_DC', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
0.64,
1.00,
0.61,
0.02,
50.00,
0.48,
1.00,
0.47,
0.06,
75.00,
0.26,
1.00,
0.28,
0.18,
90.00,
0.04,
0.85,
0.00,
0.44,
100.00,
0.00,
0.52,
0.06,
1.00,
])
cmd.volume_ramp_new('ramp_DT', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
1.00,
0.99,
0.55,
0.02,
50.00,
1.00,
0.98,
0.46,
0.06,
75.00,
1.00,
0.99,
0.37,
0.19,
90.00,
0.92,
0.92,
0.00,
0.39,
100.00,
0.76,
0.73,
0.00,
1.00,
])
cmd.volume_ramp_new('ramp_P', [
0.00,
1.00,
1.00,
1.00,
0.00,
25.00,
1.00,
0.95,
0.93,
0.02,
50.00,
1.00,
0.85,
0.69,
0.06,
75.00,
1.00,
0.78,
0.55,
0.19,
90.00,
1.00,
0.66,
0.30,
0.39,
100.00,
0.97,
0.50,
0.00,
1.00,
])
cmd.volume_ramp_new('ramp_jet', [
0.00,
0.00,
0.00,
1.00,
0.00,
25.00,
0.06,
0.93,
1.00,
0.05,
50.00,
0.49,
0.51,
1.00,
0.15,
75.00,
1.00,
1.00,
0.00,
0.23,
90.00,
0.80,
0.18,
1.00,
0.48,
100.00,
0.98,
0.01,
1.00,
1.00,
])
cmd.volume_ramp_new('ramp_delta', [
-1.0, 1.00, 0.00, 0.00, 0.00, -0.4, 1.00, 1.00, 0.00, 1.0, -0.2, 1.00,
0.00, 0.00, 0.00, 0.2, 0.00, 0.00, 1.00, 0.00, 0.4, 0.00, 1.00, 1.00,
1.0, 1.0, 0.00, 0.00, 1.00, 0.00
])
F = h5py.File(fname, 'r')
NUCS = natsort.natsorted(F.keys())
if int(top) < 1:
print('top should be greater than 1')
return
top_ = min(int(top), len(NUCS))
NUCS_ = NUCS[:top_]
for i in NUCS_:
data = F[i]['data'][()]
origin = F[i]['origin'][()]
step = F[i]['step'][()]
b = Brick.from_numpy(data, step, origin)
bname = prefix + '_' + i
cmd.load_brick(b, bname)
volname = bname + '_volume'
cmd.volume(volname, bname)
cmd.volume_color(volname, 'ramp_' + ramp)
def load_vis_map(filename, name=None, mimic=1, quiet=1, _self=cmd):
'''
DESCRIPTION
Load a map (a.k.a. volume or brick) from a vis file.
ARGUMENTS
filename = string: filename
name = string: name of map or group prefix, if ending with
a period. {default: "Dataset Name" property from file}
mimic = 0/1: load isosurfaces {default: 1}
'''
from chempy.brick import Brick
mimic, quiet = int(mimic), int(quiet)
data = get_data(filename)
try:
if data.attrs['Rank'] != 3:
raise ValueError('Rank %s' % data.attrs['Rank'])
if tuple(data.attrs['Dimensions']) != data.value.shape:
raise ValueError('Dimensions %s' % data.attrs['Dimensions'])
if data.attrs['Grid Type'] != 1:
raise ValueError('Unknown Grid Type: %s' % data.attrs['Grid Type'])
ds_name = data.attrs.get("Dataset Name") or "unnamed"
obj = Brick.from_numpy(data.value,
data.attrs["Space Ratio"],
data.attrs["Origin"])
except Exception as e:
raise CmdException('could not find map in vis file')
if not name:
name = _self.get_unused_name(ds_name, 0)
elif name.endswith("."):
name = _self.get_unused_name(name + ds_name, 0)
_self.load_brick(obj, name)
try:
cell = data.attrs['Unit Cell ABC'].tolist() + \
data.attrs['Unit Cell Angle'].tolist()
except KeyError:
cell = [False]
if all(cell):
cell.append('P 1')
_self.set_symmetry(name, *cell)
if not mimic:
return name
isofunc = {1: _self.isomesh, 2: _self.isodot}.get(
0, _self.isosurface)
for color, isolevel in zip(data.attrs.get('Contour Colors', []),
data.attrs.get('Contour Isovalues', [])):
mesh_name = _self.get_unused_name(name + '_contour', 0)
isofunc(mesh_name, name, isolevel)
apply_color(color, mesh_name, quiet, _self)
return name