def read(path):
with open(pyfs.rext(path, "hed"), "rb") as fd:
header = readHeader(fd)
with open(pyfs.rext(path, "img"), "r+b") as fd:
rows = int(header["ROWS"])
cols = int(header["COLS"])
count = int(header["IFOL"] + 1)
data = np.memmap(fd, dtype="f4", mode="c")
return data.reshape([count, cols, rows])
def topng(mrc, scale, force):
png = pyfs.rext(mrc, 'png')
png = mrc + '.png'
if not force and pyfs.exists(png):
return
print(mrc, '->', png)
image = imaging.load(mrc)[0]
image = imaging.filters.zoom(image, scale)
imaging.save(image, png)
def process(path, aligned, args, gpu):
t0 = time.time()
aligned_dw = unpack.label(aligned, 'dw')
aligned_log = pyfs.rext(aligned, 'shifts')
aligned_stk = pyfs.rext(aligned, 'mrcs')
print(path, '->', aligned)
print(' ' * len(path), '->', aligned_log)
tmpdir = tempfile.mkdtemp()
tmp_unzipped = pyfs.join(tmpdir, 'decompressed.mrc')
tmp_unpacked = pyfs.join(tmpdir, 'unpacked.mrc')
tmp_aligned = pyfs.join(tmpdir, 'aligned.mrc')
tmp_aligned_dw = pyfs.join(tmpdir, 'aligned_DW.mrc')
tmp_logfile = pyfs.join(tmpdir, 'aligned0-Full.log')
tmp_stkfile = pyfs.join(tmpdir, 'aligned_Stk.mrc')
tmp_unzipped = pbunzip2(path, tmp_unzipped)
if args.unpack:
unpack.unpack(tmp_unzipped,
tmp_unpacked,
args.defects,
args.norm,
mode='byte')
motioncor2(tmp_unpacked, tmp_aligned, args, gpu=gpu)
else:
args.mocor2_norm = args.norm
motioncor2(tmp_unzipped, tmp_aligned, args, gpu=gpu)
mv(tmp_aligned, aligned)
mv(tmp_aligned_dw, aligned_dw)
mv(tmp_logfile, aligned_log)
mv(tmp_stkfile, aligned_stk)
shutil.rmtree(tmpdir, False)
print('aligning: %s took: %.2f secs' % (path, time.time() - t0))
def motioncor2(src, dst, args, gpu=0):
print('processing: %s' % (src))
cmd = ['motioncor2']
if src.endswith('.mrc') or src.endswith('.mrcs'):
cmd += ['-InMrc', src]
elif src.endswith('.tif'):
cmd += ['-InTiff', src]
else:
raise ValueError('file: %s must be TIFF or MRC' % (src))
cmd += ['-OutMrc', dst]
cmd += ['-Bft', args.bfactor]
cmd += ['-Patch', args.patches, args.patches, 50]
cmd += ['-Kv', args.kv]
cmd += ['-PixSize', args.apix]
cmd += ['-LogFile', pyfs.rext(dst, '')]
if args.inframe:
cmd += ['-InFmMotion', 1]
if args.mag is not None:
print(args.mag)
cmd += ['-Mag', args.mag[0], args.mag[1], args.mag[2]]
if hasattr(args, 'mocor2_norm'):
cmd += ['-Gain', args.mocor2_norm]
if args.binby > 1:
cmd += ['-FtBin', args.binby]
if args.savestack:
cmd += ['-OutStack', 1]
if args.throw:
cmd += ['-Throw', args.throw]
if args.truncate:
cmd += ['-Trunc', args.truncate]
if args.correction is not None:
expf = calculate_dose(src, args.apix, args.correction)
print('using dose rate: %f e-/A^2/frame' % (expf))
cmd += ['-FmDose', expf]
group = calculate_grouping(src, args.group)
cmd += ['-Group', args.group]
if args.rotgain:
cmd += ['-RotGain', 3, '-FlipGain', 1]
cmd += ['-Gpu', gpu]
print(' '.join(map(str, cmd)))
call(cmd, stdout=None)
def save_stats(stats, path, **kwargs):
path = pyfs.rext(path, "yaml")
save(stats, path)
def load_stats(path, **kwargs):
path = pyfs.rext(path, "yaml")
print "load stat:", path
return load(path)
def load_stats(path, **kwargs):
path = pyfs.rext(path, "yaml")
return load(path)