def get_element(self, basename, file_handle):
with uff.FortranFile(file_handle.name, endian=self._endian) as uffile:
try:
leading_line = uffile.readline()
except IOError:
leading_line = ''
return leading_line
def create_bpch(filename, title=DEFAULT_TITLE, filetype=FILETYPE02, **kwargs):
"""
Create a new empty bpch file.
Parameters
----------
filename : string
name or path to the bpch file.
title : string
a title line to write in the file's header.
filetype : string
bpch file type identifier (either :attr:`bpch.FILETYPE02` or
:attr:`bpch.FILETYPE4D`).
**kwargs
extra parameters passed to :class:`pygchem.utils.uff.FortranFile`
(e.g., `endian`).
Returns
-------
bpch_file
the open file instance (:class:`pygchem.utils.uff.FortranFile` object).
"""
bpch_file = uff.FortranFile(filename, 'wb', **kwargs)
bpch_file.writeline('40s', filetype.ljust(40))
bpch_file.writeline('80s', title.ljust(80))
return bpch_file
def read_bpch(filename,
mode='rb',
skip_data=True,
diaginfo_file='',
tracerinfo_file='',
**kwargs):
"""
Read the binary punch file v2 format.
Parameters
----------
filename : string
name or path to the bpch file.
mode : {'r', 'r+', rb', 'r+b', 'a'}
file open mode (see :func:`open`). Writing only ('w' or 'wb') is not
allowed.
skip_data : bool
if True, only data block metadata will be read (it will not load data
into memory but data position and size information will be provided
in addition to metadata, so that data can further be easily loaded).
diaginfo_file : string
path to the 'diaginfo.dat' file (optional). If empty, it will look
for 'diaginfo.dat' in the same directory than `filename` or it will
take a default one.
tracerinfo_file : string
path to the 'tracerinfo.dat' file (or empty string).
**kwargs
extra parameters passed to :class:`pygchem.utils.uff.FortranFile`
(e.g., `endian`).
Returns
-------
filetype
bpch file type identifier (given in the file's header)
filetitle
title (given in the file's header)
datablocks
the list of data blocks, i.e., dictionaries with data block metadata
and data as a :class:`numpy.ndarray` object or a :class:`BPCHDataProxy`
instance if `skip_data` is True.
"""
if mode != 'a' and not mode.endswith('b'):
mode += 'b' # platform independent
if 'w' in mode:
raise ValueError("write-only mode is not allowed for reading the "
"bpch file")
dir_path = os.path.abspath(os.path.dirname(filename))
if not dir_path:
dir_path = os.getcwd()
if not tracerinfo_file:
tracerinfo_file = os.path.join(dir_path, "tracerinfo.dat")
if not os.path.exists(tracerinfo_file):
tracerinfo_file = ''
if not diaginfo_file:
diaginfo_file = os.path.join(dir_path, "diaginfo.dat")
if not os.path.exists(diaginfo_file):
diaginfo_file = ''
ctm_info = CTMDiagnosticInfo(diaginfo_file=diaginfo_file,
tracerinfo_file=tracerinfo_file)
with uff.FortranFile(filename, mode, **kwargs) as bpch_file:
datablocks = []
filetype = bpch_file.readline().strip()
fsize = os.path.getsize(filename)
filetitle = bpch_file.readline().strip()
while bpch_file.tell() < fsize:
# read first and second header line
line = bpch_file.readline('20sffii')
modelname, res0, res1, halfpolar, center180 = line
line = bpch_file.readline('40si40sdd40s7i')
category_name, number, unit, tau0, tau1, reserved = line[:6]
dim0, dim1, dim2, dim3, dim4, dim5, skip = line[6:]
# get additional metadata from tracerinfo / diaginfo
try:
cat = ctm_info.categories.select_item(category_name.strip())
cat_attr = cat.to_dict()
diag = ctm_info.diagnostics.select_item(cat.offset +
int(number))
diag_attr = diag.to_dict()
if not unit.strip(): # unit may be empty in bpch
unit = diag_attr['unit'] # but not in tracerinfo
except exceptions.SelectionMismatchError:
diag = {'name': '', 'scale': 1}
diag_attr = {}
cat_attr = {}
# parse metadata, get data or set a data proxy
if dim2 == 1:
data_shape = (dim0, dim1) # 2D field
else:
data_shape = (dim0, dim1, dim2)
from_file = os.path.abspath(filename)
file_position = bpch_file.tell()
if skip_data:
bpch_file.skipline()
data = BPCHDataProxy(data_shape, 'f', from_file,
bpch_file.endian, file_position,
diag['scale'], np.nan)
else:
data = np.array(bpch_file.readline('*f'))
data = data.reshape((dim0, dim1, dim2), order='F')
datablock = {
'number': int(number),
'name': diag['name'],
'category': category_name.strip(),
'times': (timeutil.tau2time(tau0), timeutil.tau2time(tau1)),
'modelname': modelname.strip(),
'center180': bool(center180),
'halfpolar': bool(halfpolar),
'origin': (dim3, dim4, dim5),
'resolution': (res0, res1),
'shape': data_shape,
'loaded_from_file': from_file,
'save_to_file': '',
'file_position': file_position,
'data': data,
'unit': unit.strip(),
'tracerinfo': diag_attr,
'diaginfo': cat_attr
}
datablocks.append(datablock)
return filetype, filetitle, datablocks
def load(self):
with uff.FortranFile(self.path, 'rb', self.endian) as bpch_file:
bpch_file.seek(self.file_position)
data = np.array(bpch_file.readline('*f'))
data = data.reshape(self.shape, order='F')
return data * self.scale_factor