def transform_star(df,
r,
t=None,
inplace=False,
rots=None,
invert=False,
rotate=True,
adjust_defocus=False):
"""
Transform particle angles and origins according to a rotation
matrix (in radians) and an optional translation vector.
The translation may also be given as the 4th column of a 3x4 matrix,
or as a scalar distance to be applied along the axis of rotation.
"""
assert (r.shape[0] == 3)
if r.shape[1] == 4 and t is None:
t = r[:, -1]
r = r[:, :3]
assert (r.shape == (3, 3))
assert t is None or np.isscalar(t) or len(t) == 3
if inplace:
newstar = df
else:
newstar = df.copy()
if rots is None:
rots = [
euler2rot(*np.deg2rad(row[1]))
for row in df[Relion.ANGLES].iterrows()
]
if invert:
r = r.T
newrots = [ptcl.dot(r) for ptcl in rots]
if rotate:
angles = [np.rad2deg(rot2euler(q)) for q in newrots]
newstar[Relion.ANGLES] = angles
if t is not None and np.linalg.norm(t) > 0:
if np.isscalar(t):
if invert:
tt = -np.vstack([np.squeeze(q[:, 2]) * t for q in rots])
else:
tt = np.vstack([np.squeeze(q[:, 2]) * t for q in newrots])
else:
if invert:
tt = -np.vstack([q.dot(t) for q in rots])
else:
tt = np.vstack([q.dot(t) for q in newrots])
newshifts = df[Relion.ORIGINS] + tt[:, :-1]
newstar[Relion.ORIGINS] = newshifts
if adjust_defocus:
newstar[Relion.DEFOCUSU] += tt[:, -1] * calculate_apix(df)
newstar[Relion.DEFOCUSV] += tt[:, -1] * calculate_apix(df)
newstar[Relion.DEFOCUSANGLE] = np.rad2deg(
np.arctan2(newstar[Relion.DEFOCUSV], newstar[Relion.DEFOCUSV]))
return newstar
def main(args):
meta = parse_metadata(args.input) # Read cryosparc metadata file.
meta["data_input_idx"] = [
"%.6d" % (i + 1) for i in meta["data_input_idx"]
] # Reformat particle idx for Relion.
if "data_input_relpath" not in meta.columns:
if args.data_path is None:
print(
"Data path missing, use --data-path to specify particle stack path"
)
return 1
meta["data_input_relpath"] = args.data_path
meta["data_input_relpath"] = meta["data_input_idx"].str.cat(
meta["data_input_relpath"], sep="@") # Construct _rlnImageName field.
# Take care of trivial mappings.
rlnheaders = [
general[h] for h in meta.columns
if h in general and general[h] is not None
]
star = meta[[
h for h in meta.columns if h in general and general[h] is not None
]].copy()
star.columns = rlnheaders
if "rlnRandomSubset" in star.columns:
star["rlnRandomSubset"] = star["rlnRandomSubset"].apply(
lambda x: ord(x) - 64)
if "rlnPhaseShift" in star.columns:
star["rlnPhaseShift"] = np.rad2deg(star["rlnPhaseShift"])
# general class assignments and other model parameters.
phic = meta[[h for h in meta.columns if "phiC" in h
]] # Posterior probability over class assignments.
if len(phic.columns) > 0: # Check class assignments exist in input.
# phic.columns = [int(h[21]) for h in meta.columns if "phiC" in h]
phic.columns = range(len(phic.columns))
cls = phic.idxmax(axis=1)
for p in model:
if model[p] is not None:
pspec = p.split("model")[1]
param = meta[[h for h in meta.columns if pspec in h]]
if len(param.columns) > 0:
param.columns = phic.columns
star[model[p]] = param.lookup(param.index, cls)
star[
"rlnClassNumber"] = cls + 1 # Compute most probable classes and add one for Relion indexing.
else:
for p in model:
if model[p] is not None and p in meta.columns:
star[model[p]] = meta[p]
star["rlnClassNumber"] = 1
if args.cls is not None:
star = select_classes(star, args.cls)
# Convert axis-angle representation to Euler angles (degrees).
if star.columns.intersection(angles).size == len(angles):
star[angles] = np.rad2deg(star[angles].apply(
lambda x: rot2euler(expmap(x)), axis=1, raw=True, broadcast=True))
if args.minphic is not None:
mask = np.all(phic < args.minphic, axis=1)
if args.drop_bad:
star.drop(star[mask].index,
inplace=True) # Delete low-confidence particles.
else:
star.loc[
mask,
"rlnClassNumber"] = 0 # Set low-confidence particles to dummy class.
if args.transform is not None:
r = np.array(json.loads(args.transform))
star = transform_star(star, r, inplace=True)
# Write Relion .star file with correct headers.
write_star(args.output, star, reindex=True)
return 0
def main(args):
log = logging.getLogger(__name__)
hdlr = logging.StreamHandler(sys.stdout)
log.addHandler(hdlr)
log.setLevel(logging.getLevelName(args.loglevel.upper()))
data, hdr = read(args.input, inc_header=True)
if args.half2 is not None:
half2, hdr_half2 = read(args.input, inc_header=True)
if data.shape == half2.shape:
data += half2
else:
log.error("--half2 map is not the same shape as input map!")
return 1
final = None
box = np.array([hdr[a] for a in ["nx", "ny", "nz"]])
center = box // 2
if args.fft:
if args.final_mask is not None:
final_mask = read(args.final_mask)
data *= final_mask
data_ft = vop.vol_ft(data.T, pfac=args.pfac, threads=args.threads)
np.save(args.output, data_ft)
return 0
if args.transpose is not None:
try:
tax = [np.int64(a) for a in args.transpose.split(",")]
data = np.transpose(data, axes=tax)
except:
log.error(
"Transpose axes must be comma-separated list of three integers"
)
return 1
if args.flip is not None:
if args.flip.isnumeric():
args.flip = int(args.flip)
else:
args.flip = vop.label_to_axis(args.flip)
data = np.flip(data, axis=args.flip)
if args.apix is None:
args.apix = hdr["xlen"] / hdr["nx"]
log.info("Using computed pixel size of %f Angstroms" % args.apix)
if args.normalize:
if args.diameter is not None:
if args.diameter > 1.0:
args.diameter /= args.apix * 2 # Convert Angstrom diameter to pixel radius.
if args.reference is not None:
ref, refhdr = read(args.reference, inc_header=True)
final, mu, sigma = vop.normalize(data,
ref=ref,
return_stats=True,
rmask=args.diameter)
else:
final, mu, sigma = vop.normalize(data,
return_stats=True,
rmask=args.diameter)
log.info("Mean: %f, Standard deviation: %f" % (mu, sigma))
if args.apix_out is not None:
if args.scale is not None:
log.warn("--apix-out supersedes --scale")
args.scale = args.apix / args.apix_out
elif args.scale is not None:
args.apix_out = args.apix / args.scale
elif args.boxsize is not None:
args.scale = box[0] / np.double(args.boxsize)
if args.apix_out is None:
args.apix_out = args.apix
if args.boxsize is None:
if args.scale is None:
args.boxsize = box[0]
args.scale = 1
else:
args.boxsize = np.int(box[0] * args.scale)
log.info("Volume will be scaled by %f to size %d @ %f A/px" %
(args.scale, args.boxsize, args.apix_out))
if args.target and args.transform:
log.warn(
"Target pose transformation will be applied after explicit matrix")
if args.euler is not None and (args.target is not None
or args.transform is not None):
log.warn(
"Euler transformation will be applied after target pose transformation"
)
if args.translate is not None and (args.euler is not None
or args.target is not None
or args.transform is not None):
log.warn("Translation will be applied after other transformations")
if args.origin is not None:
try:
args.origin = np.array(
[np.double(tok) for tok in args.origin.split(",")]) / args.apix
assert np.all(args.origin < box)
except:
log.error(
"Origin must be comma-separated list of x,y,z coordinates and lie within the box"
)
return 1
else:
args.origin = center
log.info("Origin set to box center, %s" % (args.origin * args.apix))
if not (args.target is None and args.euler is None and args.transform is None and args.boxsize is None) \
and vop.ismask(data) and args.spline_order != 0:
log.warn(
"Input looks like a mask, --spline-order 0 (nearest neighbor) is recommended"
)
if args.transform is not None:
try:
args.transform = np.array(json.loads(args.transform))
except:
log.error("Transformation matrix must be in JSON/Numpy format")
return 1
r = args.transform[:, :3]
if args.transform.shape[1] == 4:
t = args.transform[:, -1] / args.apix
t = r.dot(args.origin) + t - args.origin
t = -r.T.dot(t)
else:
t = 0
log.debug("Final rotation: %s" % str(r).replace("\n", "\n" + " " * 16))
log.debug("Final translation: %s (%f px)" %
(str(t), np.linalg.norm(t)))
data = vop.resample_volume(data,
r=r,
t=t,
ori=None,
order=args.spline_order,
invert=args.invert)
if args.target is not None:
try:
args.target = np.array(
[np.double(tok) for tok in args.target.split(",")]) / args.apix
except:
log.error(
"Standard pose target must be comma-separated list of x,y,z coordinates"
)
return 1
args.target -= args.origin
args.target = np.where(np.abs(args.target) < 1, 0, args.target)
ori = None if args.origin is center else args.origin - center
r = vec2rot(args.target)
t = np.linalg.norm(args.target)
log.info("Euler angles are %s deg and shift is %f px" %
(np.rad2deg(rot2euler(r)), t))
log.debug("Final rotation: %s" % str(r).replace("\n", "\n" + " " * 16))
log.debug("Final translation: %s (%f px)" %
(str(t), np.linalg.norm(t)))
data = vop.resample_volume(data,
r=r,
t=args.target,
ori=ori,
order=args.spline_order,
invert=args.invert)
if args.euler is not None:
try:
args.euler = np.deg2rad(
np.array([np.double(tok) for tok in args.euler.split(",")]))
except:
log.error(
"Eulers must be comma-separated list of phi,theta,psi angles")
return 1
r = euler2rot(*args.euler)
offset = args.origin - 0.5
offset = offset - r.T.dot(offset)
data = affine_transform(data,
r.T,
offset=offset,
order=args.spline_order)
if args.translate is not None:
try:
args.translate = np.array(
[np.double(tok)
for tok in args.translate.split(",")]) / args.apix
except:
log.error(
"Translation vector must be comma-separated list of x,y,z coordinates"
)
return 1
args.translate -= args.origin
data = shift(data, -args.translate, order=args.spline_order)
if final is None:
final = data
if args.final_mask is not None:
final_mask = read(args.final_mask)
final *= final_mask
if args.scale != 1 or args.boxsize != box[0]:
final = vop.resample_volume(final,
scale=args.scale,
output_shape=args.boxsize,
order=args.spline_order)
write(args.output, final, psz=args.apix_out)
return 0
def main(args):
log = logging.getLogger(__name__)
log.setLevel(logging.INFO)
hdlr = logging.StreamHandler(sys.stdout)
if args.quiet:
hdlr.setLevel(logging.ERROR)
elif args.verbose:
hdlr.setLevel(logging.INFO)
else:
hdlr.setLevel(logging.WARN)
log.addHandler(hdlr)
data, hdr = read(args.input, inc_header=True)
final = None
box = np.array([hdr[a] for a in ["nx", "ny", "nz"]])
center = box // 2
if args.fft:
data_ft = vop.vol_ft(data.T, threads=args.threads)
np.save(args.output, data_ft)
return 0
if args.transpose is not None:
try:
tax = [np.int64(a) for a in args.transpose.split(",")]
data = np.transpose(data, axes=tax)
except:
log.error(
"Transpose axes must be comma-separated list of three integers"
)
return 1
if args.normalize:
if args.reference is not None:
ref, refhdr = read(args.reference, inc_header=True)
final, mu, sigma = vop.normalize(data, ref=ref, return_stats=True)
else:
final, mu, sigma = vop.normalize(data, return_stats=True)
final = (data - mu) / sigma
if args.verbose:
log.info("Mean: %f, Standard deviation: %f" % (mu, sigma))
if args.apix is None:
args.apix = hdr["xlen"] / hdr["nx"]
log.info("Using computed pixel size of %f Angstroms" % args.apix)
if args.target and args.matrix:
log.warn(
"Target pose transformation will be applied after explicit matrix")
if args.euler is not None and (args.target is not None
or args.matrix is not None):
log.warn(
"Euler transformation will be applied after target pose transformation"
)
if args.translate is not None and (args.euler is not None or args.target
is not None or args.matrix is not None):
log.warn("Translation will be applied after other transformations")
if args.origin is not None:
try:
args.origin = np.array(
[np.double(tok) for tok in args.origin.split(",")]) / args.apix
assert np.all(args.origin < box)
except:
log.error(
"Origin must be comma-separated list of x,y,z coordinates and lie within the box"
)
return 1
else:
args.origin = center
log.info("Origin set to box center, %s" % (args.origin * args.apix))
if not (args.target is None and args.euler is None and args.matrix is None and args.boxsize is None) \
and vop.ismask(data) and args.spline_order != 0:
log.warn(
"Input looks like a mask, --spline-order 0 (nearest neighbor) is recommended"
)
if args.matrix is not None:
try:
r = np.array(json.loads(args.matrix))
except:
log.error("Matrix format is incorrect")
return 1
data = vop.resample_volume(data,
r=r,
t=None,
ori=None,
order=args.spline_order)
if args.target is not None:
try:
args.target = np.array(
[np.double(tok) for tok in args.target.split(",")]) / args.apix
except:
log.error(
"Standard pose target must be comma-separated list of x,y,z coordinates"
)
return 1
args.target -= args.origin
args.target = np.where(np.abs(args.target) < 1, 0, args.target)
ori = None if args.origin is center else args.origin - args.center
r = vec2rot(args.target)
t = np.linalg.norm(args.target)
log.info("Euler angles are %s deg and shift is %f px" %
(np.rad2deg(rot2euler(r)), t))
data = vop.resample_volume(data,
r=r,
t=args.target,
ori=ori,
order=args.spline_order,
invert=args.target_invert)
if args.euler is not None:
try:
args.euler = np.deg2rad(
np.array([np.double(tok) for tok in args.euler.split(",")]))
except:
log.error(
"Eulers must be comma-separated list of phi,theta,psi angles")
return 1
r = euler2rot(*args.euler)
offset = args.origin - 0.5
offset = offset - r.T.dot(offset)
data = affine_transform(data,
r.T,
offset=offset,
order=args.spline_order)
if args.translate is not None:
try:
args.translate = np.array(
[np.double(tok)
for tok in args.translate.split(",")]) / args.apix
except:
log.error(
"Translation vector must be comma-separated list of x,y,z coordinates"
)
return 1
args.translate -= args.origin
data = shift(data, -args.translate, order=args.spline_order)
if args.boxsize is not None:
args.boxsize = np.double(args.boxsize)
data = zoom(data, args.boxsize / box, order=args.spline_order)
args.apix = args.apix * box[0] / args.boxsize
if final is None:
final = data
if args.final_mask is not None:
final_mask = read(args.final_mask)
final *= final_mask
write(args.output, final, psz=args.apix)
return 0
def test_rot2euler(self):
e1test = util.rot2euler(r1)
self.assertTrue(np.array_equal(e1, e1test))
e2test = util.rot2euler(r3)
self.assertTrue(np.allclose(e3, e2test))
def main(args):
meta = parse_metadata(args.input) # Read cryosparc metadata file.
meta["data_input_idx"] = [
"%.6d" % (i + 1) for i in meta["data_input_idx"]
] # Reformat particle idx for Relion.
if "data_input_relpath" not in meta.columns:
if args.data_path is None:
print(
"Data path missing, use --data-path to specify particle stack path"
)
return 1
meta["data_input_relpath"] = args.data_path
meta["data_input_relpath"] = meta["data_input_idx"].str.cat(
meta["data_input_relpath"], sep="@") # Construct rlnImageName field.
# Take care of trivial mappings.
rlnheaders = [
general[h] for h in meta.columns
if h in general and general[h] is not None
]
df = meta[[
h for h in meta.columns if h in general and general[h] is not None
]].copy()
df.columns = rlnheaders
if "rlnRandomSubset" in df.columns:
df["rlnRandomSubset"] = df["rlnRandomSubset"].apply(
lambda x: ord(x) - 64)
if "rlnPhaseShift" in df.columns:
df["rlnPhaseShift"] = np.rad2deg(df["rlnPhaseShift"])
# Class assignments and other model parameters.
phic = meta[[h for h in meta.columns if "phiC" in h
]] # Posterior probability over class assignments.
if len(phic.columns) > 0: # Check class assignments exist in input.
# phic.columns = [int(h[21]) for h in meta.columns if "phiC" in h]
phic.columns = range(len(phic.columns))
cls = phic.idxmax(axis=1)
for p in model:
if model[p] is not None:
pspec = p.split("model")[1]
param = meta[[h for h in meta.columns if pspec in h]]
if len(param.columns) > 0:
param.columns = phic.columns
df[model[p]] = param.lookup(param.index, cls)
df["rlnClassNumber"] = cls + 1 # Add one for Relion indexing.
else:
for p in model:
if model[p] is not None and p in meta.columns:
df[model[p]] = meta[p]
df["rlnClassNumber"] = 1
if args.cls is not None:
df = star.select_classes(df, args.cls)
# Convert axis-angle representation to Euler angles (degrees).
if df.columns.intersection(star.Relion.ANGLES).size == len(
star.Relion.ANGLES):
df[star.Relion.ANGLES] = np.rad2deg(df[star.Relion.ANGLES].apply(
lambda x: rot2euler(expmap(x)), axis=1, raw=True, broadcast=True))
if args.minphic is not None:
mask = np.all(phic < args.minphic, axis=1)
if args.keep_bad:
df.loc[mask, "rlnClassNumber"] = 0
else:
df.drop(df[mask].index, inplace=True)
if args.copy_micrograph_coordinates is not None:
coord_star = pd.concat(
(star.parse_star(inp, keep_index=False)
for inp in glob(args.copy_micrograph_coordinates)),
join="inner")
df = star.smart_merge(df,
coord_star,
fields=star.Relion.MICROGRAPH_COORDS)
if args.transform is not None:
r = np.array(json.loads(args.transform))
df = star.transform_star(df, r, inplace=True)
# Write Relion .star file with correct headers.
star.write_star(args.output, df, reindex=True)
return 0