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in_out.py
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in_out.py
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from string import ascii_letters,digits
import os,glob,crystals,hashlib,numpy as np
from subprocess import check_output,Popen,PIPE
from crystals import Crystal as Crys
from utils import glob_colors as colors
from EDutils import felix as fe #;imp.reload(fe)
from EDutils import pets #;imp.reload(pets)
from EDutils import dials_utils as dials#;imp.reload(dials)
from EDutils import xds #;imp.reload(xds)
from EDutils import readers
chars = ascii_letters+digits
mol_path=lambda mol:'static/data/%s' %mol
get_path = lambda mol,key,frame_str:os.path.join(mol_path(mol),key,frame_str)
#data processing paths
pets_path = lambda mol:os.path.join(mol_path(mol),'pets')#,'%s.pts' %mol)
dials_path = lambda mol:os.path.join(mol_path(mol),'dials')
xds_path = lambda mol:os.path.join(mol_path(mol),'xds','XDS_ASCII.HKL')
dat_path = lambda mol:os.path.join(mol_path(mol),'dat')
tmp_dat_folder = lambda session:os.path.join(session['path'],'tmp_dat')
proc_dat_files = {
'xds' : ['XDS_ASCII.HKL'],
'pets' : ['*.pts','*.rpl','*.xyz','*.cor','*.hkl','*.cenloc','*.cif_pets','*_dyn.cif_pets','*.cif'],
'dials': ['*.expt', '*.refl','reflections.txt'],
}
p_open=lambda cmd:Popen(cmd,shell=True,stdout=PIPE,stderr=PIPE)
short_hash=lambda s:hashlib.shake_256(s.encode('utf-8')).hexdigest(5)
def get_frames_fmt(path):
'''return the type of frames in the folder if any '''
fmts = readers.fmts
files = glob.glob(os.path.join(path,'*.*'))
if not len(files):return ''
#detect format
fmt,i = '',0
while fmt not in fmts and i<len(files):
fmt = files[i].split('.')[-1]
i+=1
if fmt not in fmts:fmt =""
return fmt
def get_local_frames_folder():
local_frames_link='static/database'
if not os.path.exists(local_frames_link):
print(colors.red,'Creating database folder for storing experimental data frames.',colors.black)
cmd="mkdir database; ln -s $(realpath database) {dest}".format(dest=local_frames_link)
check_output(cmd,shell=True).decode().strip()
local_frames_path=check_output("realpath $(readlink %s)" %local_frames_link,shell=True).decode().strip()
if not os.path.exists(os.path.join(local_frames_path,'frames_test')):
cmd="cp static/spg/frames_test.zip {path}/; cd {path}; unzip frames_test.zip -d frames_test;rm frames_test.zip ".format(path=local_frames_path)
o=check_output(cmd,shell=True).decode()
print(colors.red,'Created frames_test folder in database.',colors.black)
return local_frames_path
local_frames_path = get_local_frames_folder()
def check_proc_data(path):
missing_files='?'
dtype='unknown'
for dat_type,dat_files in proc_dat_files.items():
files = np.array([len(glob.glob(os.path.join(path,f)))>=1
for f in dat_files])
if ~all(files) and any(files):
dtype=dat_type
missing_files=', '.join(np.array(dat_files)[~files])
if all(files):
dtype=dat_type;
missing_files=''
break
return {'dat_type':dtype,'missing_files':missing_files}
### simulations paths
get_pkl = lambda id:'static/data/tmp/%s/b.pkl' %id
rock_path = lambda id:'static/data/tmp/%s/rock_.pkl' %id
felix_path = lambda mol:os.path.join(mol_path(mol),'felix')
felix_pkl = lambda session:os.path.join(felix_path(session['mol']),'felix.pkl')
sim_path = lambda mol:os.path.join(mol_path(mol),'rocks')
def data_path(link):
filename=os.path.basename(link.replace('?download=1',''))
fmt=get_compressed_fmt(filename) #;print('fmt:',fmt)
#not good but should work
if fmt:
record=''
if 'zenodo.org' in link :
# print(link.split('record/'))
record=link.split('record/')[1].split('/files')[0]
elif 'http' in link:
record=link.split('/')[2].replace('.','_').replace(':','_')
folder='%s_%s' %(record,filename)
else:
folder=filename
folder=folder.replace('.%s' %fmt,'')
return 'static/database/%s' %folder
uncompress_fmts={
'zip' :'unzip',
# 'h5' :'',
'bz2' :'bunzip2',
'rar' :'unrar',
'tar' :'tar -xvf',
'ser.bz2' :'bunzip2',
'tar.bz2' :'tar -xvjf',
'tar.gz' :'tar -xvzf',
'tar.xz' :'tar -xJf',
# 'LP' :'',
# 'LP.bz2' :''
}
compress_fmts = list(uncompress_fmts.keys())
def get_compressed_fmt(link):
filename=os.path.basename(link.replace('?download=1','')) #;print(filename)
fmts=[fmt for fmt in compress_fmts if fmt in filename] #;print(fmts)
if len(fmts)==1:
return fmts[0]
elif len(fmts)>1:
return fmts[-1]
else:
return ''
pets_data={}
def get_frames_folder(mol,frame_type,full=False):
'''get the actual name of the frames folder as defined in the database
- full :
True : returns the whole path from the database root folder
False : returns the basename of the folder only
'''
folder=""
frame_path = os.path.join(mol_path(mol),frame_type)
if os.path.exists(frame_path):
if full:
cmd = "readlink %s" %frame_path
folder=check_output(cmd,shell=True).decode().strip()
# ;print('folder : ' ,folder)
folder=folder.replace('%s' %local_frames_path,'')#.split(';')[1]
else:
cmd = "basename `readlink %s`" %frame_path
folder=check_output(cmd,shell=True).decode().strip()
return folder
def get_dat_types(mol):
dat_types = [dat_type for dat_type in ['dials','pets','xds']
if os.path.exists(os.path.join(mol_path(mol),dat_type))]
return dat_types
def load_dat_type(mol):
dat_type = get_dat_type(mol) #;print(dat_type)
if dat_type=='dials':
pets_data[mol]=dials.Dials(dials_path(mol))
elif dat_type=='pets':
pets_data[mol]=pets.Pets(path=pets_path(mol),gen=False,dyn=0)
elif dat_type=='xds':
pets_data[mol]=xds.XDS(xds_path(mol))
# print(list(pets_data.keys()))
print(colors.green+'processed data type for structure %s : %s' %(mol,dat_type)+colors.black)
return dat_type
def get_dat_type(mol):
dat_type=None
if os.path.exists(dat_path(mol)):
cmd = 'basename `readlink %s`' %dat_path(mol) #;print(cmd)
dat_type = check_output(cmd,shell=True).decode().strip()#;print(dat_type)
return dat_type
def select_dat_type(mol,dat_type):
cmd = 'cd {mol_path};if [ -L dat ];then rm dat;fi;ln -s {dat_type} dat'.format(
dat_type = dat_type,
mol_path = mol_path(mol),
)
out = check_output(cmd,shell=True).decode().strip();print(out)
def update_exp_data(mol):
dat_type=''
dat_types=get_dat_types(mol)
if len(dat_types):
#if data are available but no link is found,
#create one for the first available data
if not os.path.exists(dat_path(mol)):
select_dat_type(mol,dat_types[0])
dat_type=load_dat_type(mol)
return dat_type
def load_felix(session):
if not os.path.exists(felix_pkl(session)):
# felix_path = os.path.dirname(felix_pkl(session['mol']))
# print(colors.red+felix_path+colors.black)
# print(glob.glob(felix_path+'/*_dyn.cif_pets'))
fe.Felix(felix_path(session['mol']),session['mol'])
# out=check_output("ln -s %s/felix.pkl %s" %(felix_path,mol_path(session['mol'])),shell=True).decode()
# if out:print(out)
print(colors.red+'felix created sucessfully'+colors.black)
return fe.load_felix(felix_path(session['mol']))
def get_structures():
structures =[os.path.basename(s)
for s in glob.glob("static/data/*") if not s=="static/data/tmp"]
return structures
builtins = crystals.Crystal.builtins
gifs = {os.path.basename(s)[:-4]:s for s in glob.glob("static/gifs/*")}
fig_wh=725
dummy_crys = dict(zip(
['file','a','b','c','alpha','beta','gamma','a1', 'a2', 'a3','chemical_formula',
'nb_atoms','lattice_system'],
['?']*13))
dummy_crys['spg_ref']=False
def b_str(x,i):
if i:
n=10**i
return str(tuple(np.round(np.array(x)*n)/n))[1:-1]
else:
return str(tuple(x))[1:-1]
return
def b_arr(x,x0):
try :
y = np.array(x.split(","), dtype=float).tolist()
if not len(y)==3:y=list(x0)
return y
except:
return list(x0)
def create_id():
id=''.join([chars[s] for s in np.random.randint(0,len(chars),10)])
return id
def normalize(s):
'''to use it as marker size data are positive and the mean should be around 30'''
s+=-s.min()
s/=s.max()
s*=30
# s = (s-s.min())/s.max()*30
return s