def open(cls, obj, nids=None, **kwargs):
"""
Flexible constructor. obj can be a :class:`Flow` or a string with the directory containing the Flow.
nids is an optional list of :class:`Node` identifiers used to filter the set of :class:`Task` in the Flow.
"""
has_dirpath = False
if is_string(obj):
try:
obj = Flow.pickle_load(obj)
except:
has_dirpath = True
if not has_dirpath:
# We have a Flow. smeth is the name of the Task method used to open the file.
items = []
smeth = "open_" + cls.EXT.lower()
for task in obj.iflat_tasks(nids=nids): #, status=obj.S_OK):
open_method = getattr(task, smeth, None)
if open_method is None: continue
ncfile = open_method()
if ncfile is not None: items.append((task.pos_str, ncfile))
return cls(*items)
else:
# directory --> search for files with the appropriate extension and open it with abiopen.
if nids is not None: raise ValueError("nids cannot be used when obj is a directory.")
return cls.from_dir(obj)
def abiopen(filepath):
"""
Factory function that opens any file supported by abipy.
File type is detected from the extension
Args:
filepath: string with the filename.
"""
if os.path.basename(filepath) == "__AbinitFlow__.pickle":
return Flow.pickle_load(filepath)
cls = abifile_subclass_from_filename(filepath)
return cls.from_file(filepath)
def abiopen(filepath):
"""
Factory function that opens any file supported by abipy.
File type is detected from the extension
Args:
filepath: string with the filename.
"""
if os.path.basename(filepath) == "__AbinitFlow__.pickle":
return Flow.pickle_load(filepath)
# Handle old output files produced by Abinit.
import re
outnum = re.compile(".+\.out[\d]+")
abonum = re.compile(".+\.abo[\d]+")
if outnum.match(filepath) or abonum.match(filepath):
return AbinitOutputFile.from_file(filepath)
cls = abifile_subclass_from_filename(filepath)
return cls.from_file(filepath)
def abiopen(filepath):
"""
Factory function that opens any file supported by abipy.
File type is detected from the extension
Args:
filepath: string with the filename.
"""
if os.path.basename(filepath) == "__AbinitFlow__.pickle":
return Flow.pickle_load(filepath)
# Handle old output files produced by Abinit.
import re
outnum = re.compile(".+\.out[\d]+")
abonum = re.compile(".+\.abo[\d]+")
if outnum.match(filepath) or abonum.match(filepath):
return AbinitOutputFile.from_file(filepath)
cls = abifile_subclass_from_filename(filepath)
return cls.from_file(filepath)
def open(cls, obj, nids=None, **kwargs):
"""
Flexible constructor. obj can be a :class:`Flow` or a string with the directory containing the Flow.
nids is an optional list of :class:`Node` identifiers used to filter the set of :class:`Task` in the Flow.
"""
has_dirpath = False
if is_string(obj):
try:
obj = Flow.pickle_load(obj)
except:
has_dirpath = True
items = []
if not has_dirpath:
# We have a Flow. smeth is the name of the Task method used to open the file.
smeth = "open_" + cls.EXT.lower()
for task in obj.iflat_tasks(nids=nids): #, status=obj.S_OK):
open_method = getattr(task, smeth, None)
if open_method is None: continue
ncfile = open_method()
if ncfile is not None: items.append((task.pos_str, ncfile))
else:
# directory --> search for files with the appropriate extension and open it with abiopen.
if nids is not None: raise ValueError("nids cannot be used when obj is a directory.")
from abipy.abilab import abiopen
for dirpath, dirnames, filenames in os.walk(obj):
filenames = [f for f in filenames if f.endswith(cls.EXT + ".nc") or f.endswith(cls.EXT)]
for f in filenames:
ncfile = abiopen(os.path.join(dirpath, f))
if ncfile is not None: items.append((ncfile.filepath, ncfile))
new = cls(*items)
# Save a reference to the initial object so that we can reload it if needed
#new._initial_object = obj
return new