mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-10-02 06:21:05 +02:00
implement TREXIO File class and change import of pytrexio module
This commit is contained in:
parent
4c28a4cac8
commit
7b5ebf6272
@ -9,7 +9,7 @@ import trexio as tr
|
||||
#=========================================================#
|
||||
|
||||
# 0: TREXIO_HDF5 ; 1: TREXIO_TEXT
|
||||
TEST_TREXIO_BACKEND = tr.TREXIO_HDF5
|
||||
TEST_TREXIO_BACKEND = tr.TREXIO_TEXT
|
||||
OUTPUT_FILENAME_TEXT = 'test_py_swig.dir'
|
||||
OUTPUT_FILENAME_HDF5 = 'test_py_swig.h5'
|
||||
|
||||
@ -37,7 +37,8 @@ except:
|
||||
#=========================================================#
|
||||
|
||||
# create TREXIO file and open it for writing
|
||||
test_file = tr.open(output_filename, 'w', TEST_TREXIO_BACKEND)
|
||||
#test_file = tr.open(output_filename, 'w', TEST_TREXIO_BACKEND)
|
||||
test_file = tr.File(output_filename, mode='w', back_end=TEST_TREXIO_BACKEND)
|
||||
|
||||
# Print docstring of the tr.open function
|
||||
#print(tr.open.__doc__)
|
||||
@ -107,15 +108,19 @@ labels = [
|
||||
tr.write_nucleus_label(test_file,labels)
|
||||
|
||||
# close TREXIO file
|
||||
tr.close(test_file)
|
||||
|
||||
# [TODO:] this functional call is no longer needed as we introduced TREXIO_File class which has a desctructor that closes the file
|
||||
#tr.close(test_file)
|
||||
# [TODO:] without calling destructor on test_file the TREXIO_FILE is not getting created and the data is not written when using TEXT back end. This, the user still has to explicitly call destructor on test_file object instead
|
||||
# tr.close function. This is only an issue when the data is getting written and read in the same session (e.g. in Jupyter notebook)
|
||||
del test_file
|
||||
|
||||
#==========================================================#
|
||||
#============ READ THE DATA FROM THE TEST FILE ============#
|
||||
#==========================================================#
|
||||
|
||||
# open previously created TREXIO file, now in 'read' mode
|
||||
test_file2 = tr.open(output_filename, 'r', TEST_TREXIO_BACKEND)
|
||||
#test_file2 = tr.open(output_filename, 'r', TEST_TREXIO_BACKEND)
|
||||
test_file2 = tr.File(output_filename, 'r', TEST_TREXIO_BACKEND)
|
||||
|
||||
# read nucleus_num from file
|
||||
rnum = tr.read_nucleus_num(test_file2)
|
||||
@ -164,7 +169,7 @@ rpoint_group = tr.read_nucleus_point_group(test_file2)
|
||||
assert rpoint_group==point_group
|
||||
|
||||
# close TREXIO file
|
||||
tr.close(test_file2)
|
||||
#tr.close(test_file2)
|
||||
|
||||
# cleaning (remove the TREXIO file)
|
||||
try:
|
||||
|
||||
@ -92,7 +92,7 @@ Moreover, exception handling becomes trivial thanks to the use of TREXIO exit co
|
||||
|
||||
|
||||
try:
|
||||
from pytrexio.pytrexio import *
|
||||
import pytrexio.pytrexio as pytr
|
||||
except ImportError:
|
||||
raise Exception("Could not import pytrexio module from trexio package")
|
||||
|
||||
@ -558,6 +558,76 @@ struct trexio_s {
|
||||
char padding[6]; /* Ensures the proper alignment of back ends */
|
||||
};
|
||||
#+end_src
|
||||
|
||||
*** TREXIO_File Python class
|
||||
|
||||
#+begin_src python :tangle basic_python.py
|
||||
class File:
|
||||
"""TREXIO File object.
|
||||
|
||||
General information about the TREXIO file.
|
||||
|
||||
Parameters:
|
||||
|
||||
filename: str
|
||||
Is a name of the full path to the TREXIO file.
|
||||
back_end: int
|
||||
One of the currently supported TREXIO back ends.
|
||||
For example, TREXIO_HDF5 (0) or TREXIO_TEXT (1).
|
||||
mode: str
|
||||
One of the currently supported TREXIO open modes.
|
||||
For example, 'r' or 'w'.
|
||||
isOpen: bool
|
||||
Flag indicating whether the current object is still open for I/O
|
||||
pytrexio_s:
|
||||
A PyObject corresponding to SWIG proxy of the trexio_s struct in C.
|
||||
This argument is in fact a TREXIO file handle, which is required for
|
||||
communicating with the C back end.
|
||||
info: dict
|
||||
Dictionary of key-value pairs with additional information about the file.
|
||||
"""
|
||||
|
||||
|
||||
def __init__(self, filename, mode='r', back_end=TREXIO_HDF5,
|
||||
pytrexio_s=None, info=None):
|
||||
"""This is a TREXIO File constructor."""
|
||||
|
||||
self.filename = filename
|
||||
self.mode = mode
|
||||
self.back_end = back_end
|
||||
|
||||
self.isOpen = False
|
||||
if pytrexio_s is None:
|
||||
self.pytrexio_s = open(filename, mode, back_end)
|
||||
self.isOpen = True
|
||||
else:
|
||||
self.pytrexio_s = pytrexio_s
|
||||
self.isOpen = None
|
||||
|
||||
self.info = info
|
||||
|
||||
|
||||
def close(self):
|
||||
"""Close a TREXIO File."""
|
||||
|
||||
if self.isOpen:
|
||||
close(self.pytrexio_s)
|
||||
self.isOpen = False
|
||||
else:
|
||||
raise Exception("TREXIO File object has not been opened.")
|
||||
|
||||
|
||||
def __del__(self):
|
||||
"""This is a TREXIO File destructor."""
|
||||
|
||||
if self.isOpen:
|
||||
close(self.pytrexio_s)
|
||||
elif self.isOpen is None:
|
||||
raise Exception("[WIP]: TREXIO file handle provided but what if the file is already closed?")
|
||||
else:
|
||||
pass
|
||||
#+end_src
|
||||
|
||||
** Polymorphism of the file handle
|
||||
|
||||
Polymorphism of the ~trexio_t~ type is handled by ensuring that the
|
||||
@ -767,7 +837,7 @@ end interface
|
||||
|
||||
*** Python
|
||||
|
||||
#+begin_src c :tangle basic_python.py
|
||||
#+begin_src python :tangle basic_python.py
|
||||
def open(file_name: str, mode: str, back_end: int):
|
||||
"""Create TREXIO file or open existing one.
|
||||
|
||||
@ -790,9 +860,8 @@ def open(file_name: str, mode: str, back_end: int):
|
||||
>>> trex_file = tr_open("example.h5", "w", TREXIO_HDF5)
|
||||
"""
|
||||
|
||||
|
||||
try:
|
||||
trexio_file = trexio_open(file_name, mode, back_end)
|
||||
trexio_file = pytr.trexio_open(file_name, mode, back_end)
|
||||
assert trexio_file is not None
|
||||
except AssertionError:
|
||||
raise Exception(f"Could not open TREXIO file {file_name} using trexio_open function. Please make sure that there are no typos in the file name.")
|
||||
@ -924,19 +993,18 @@ end interface
|
||||
|
||||
*** Python
|
||||
|
||||
#+begin_src c :tangle basic_python.py
|
||||
#+begin_src python :tangle basic_python.py
|
||||
def close(trexio_file):
|
||||
"""Close TREXIO file.
|
||||
|
||||
Parameter is a ~trexio_file~ object that has been created by a call to ~open~ function.
|
||||
"""
|
||||
|
||||
|
||||
try:
|
||||
rc = trexio_close(trexio_file)
|
||||
rc = pytr.trexio_close(trexio_file)
|
||||
assert rc==TREXIO_SUCCESS
|
||||
except AssertionError:
|
||||
raise Exception(trexio_string_of_error(rc))
|
||||
raise Exception(pytr.trexio_string_of_error(rc))
|
||||
#+end_src
|
||||
|
||||
* Templates for front end
|
||||
@ -1292,7 +1360,7 @@ def write_$group_num$(trexio_file, num_w: int) -> None:
|
||||
Parameters:
|
||||
|
||||
trexio_file:
|
||||
TREXIO file handle.
|
||||
TREXIO File object.
|
||||
|
||||
num_w: int
|
||||
Value of the $group_num$ variable to be written.
|
||||
@ -1302,12 +1370,11 @@ def write_$group_num$(trexio_file, num_w: int) -> None:
|
||||
- Exception from some other error (e.g. RuntimeError).
|
||||
"""
|
||||
|
||||
|
||||
try:
|
||||
rc = trexio_write_$group_num$(trexio_file, num_w)
|
||||
rc = pytr.trexio_write_$group_num$(trexio_file.pytrexio_s, num_w)
|
||||
assert rc==TREXIO_SUCCESS
|
||||
except AssertionError:
|
||||
raise Exception(trexio_string_of_error(rc))
|
||||
raise Exception(pytr.trexio_string_of_error(rc))
|
||||
except:
|
||||
raise
|
||||
|
||||
@ -1317,7 +1384,7 @@ def write_$group_num$(trexio_file, num_w: int) -> None:
|
||||
def read_$group_num$(trexio_file) -> int:
|
||||
"""Read the $group_num$ variable from the TREXIO file.
|
||||
|
||||
Parameter is a ~trexio_file~ object that has been created by a call to ~open~ function.
|
||||
Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
|
||||
|
||||
Returns:
|
||||
~num_r~: int
|
||||
@ -1328,12 +1395,11 @@ def read_$group_num$(trexio_file) -> int:
|
||||
- Exception from some other error (e.g. RuntimeError).
|
||||
"""
|
||||
|
||||
|
||||
try:
|
||||
rc, num_r = trexio_read_$group_num$(trexio_file)
|
||||
rc, num_r = pytr.trexio_read_$group_num$(trexio_file.pytrexio_s)
|
||||
assert rc==TREXIO_SUCCESS
|
||||
except AssertionError:
|
||||
raise Exception(trexio_string_of_error(rc))
|
||||
raise Exception(pytr.trexio_string_of_error(rc))
|
||||
except:
|
||||
raise
|
||||
|
||||
@ -1884,7 +1950,7 @@ def write_$group_dset$(trexio_file, dset_w) -> None:
|
||||
Parameters:
|
||||
|
||||
trexio_file:
|
||||
TREXIO file handle.
|
||||
TREXIO File object.
|
||||
|
||||
dset_w: list OR numpy.ndarray
|
||||
Array of $group_dset$ values to be written. If array data type does not correspond to int64 or float64, the conversion is performed.
|
||||
@ -1894,9 +1960,8 @@ def write_$group_dset$(trexio_file, dset_w) -> None:
|
||||
- Exception from some other error (e.g. RuntimeError).
|
||||
"""
|
||||
|
||||
|
||||
cutPrecision = False
|
||||
if not isinstance(dset_w, list):
|
||||
if not isinstance(dset_w, (list, tuple)):
|
||||
try:
|
||||
import numpy as np
|
||||
except ImportError:
|
||||
@ -1908,7 +1973,6 @@ def write_$group_dset$(trexio_file, dset_w) -> None:
|
||||
|
||||
if cutPrecision:
|
||||
try:
|
||||
# TODO: we have to make sure that this conversion does not introduce any noise in the data.
|
||||
dset_64 = np.$group_dset_py_dtype$64(dset_w)
|
||||
except:
|
||||
raise
|
||||
@ -1916,13 +1980,13 @@ def write_$group_dset$(trexio_file, dset_w) -> None:
|
||||
|
||||
try:
|
||||
if cutPrecision:
|
||||
rc = trexio_write_safe_$group_dset$_64(trexio_file, dset_64)
|
||||
rc = pytr.trexio_write_safe_$group_dset$_64(trexio_file.pytrexio_s, dset_64)
|
||||
else:
|
||||
rc = trexio_write_safe_$group_dset$_64(trexio_file, dset_w)
|
||||
rc = pytr.trexio_write_safe_$group_dset$_64(trexio_file.pytrexio_s, dset_w)
|
||||
|
||||
assert rc==TREXIO_SUCCESS
|
||||
except AssertionError:
|
||||
raise Exception(trexio_string_of_error(rc))
|
||||
raise Exception(pytr.trexio_string_of_error(rc))
|
||||
except:
|
||||
raise
|
||||
|
||||
@ -1935,7 +1999,7 @@ def read_$group_dset$(trexio_file, dim = None, dtype = None):
|
||||
Parameters:
|
||||
|
||||
trexio_file:
|
||||
TREXIO file handle.
|
||||
TREXIO File object.
|
||||
|
||||
dim (Optional): int
|
||||
Size of the block to be read from the file (i.e. how many items of $group_dset$ will be returned)
|
||||
@ -1952,7 +2016,6 @@ def read_$group_dset$(trexio_file, dim = None, dtype = None):
|
||||
- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
|
||||
- Exception from some other error (e.g. RuntimeError).
|
||||
"""
|
||||
|
||||
|
||||
# if dim is not specified, read dimensions from the TREXIO file
|
||||
if dim is None:
|
||||
@ -1965,10 +2028,10 @@ def read_$group_dset$(trexio_file, dim = None, dtype = None):
|
||||
|
||||
|
||||
try:
|
||||
rc, dset_64 = trexio_read_safe_$group_dset$_64(trexio_file, dim)
|
||||
rc, dset_64 = pytr.trexio_read_safe_$group_dset$_64(trexio_file.pytrexio_s, dim)
|
||||
assert rc==TREXIO_SUCCESS
|
||||
except AssertionError:
|
||||
raise Exception(trexio_string_of_error(rc))
|
||||
raise Exception(pytr.trexio_string_of_error(rc))
|
||||
except:
|
||||
raise
|
||||
|
||||
@ -2465,7 +2528,7 @@ def write_$group_dset$(trexio_file, dset_w: list) -> None:
|
||||
Parameters:
|
||||
|
||||
trexio_file:
|
||||
TREXIO file handle.
|
||||
TREXIO File object.
|
||||
|
||||
dset_w: list
|
||||
Array of $group_dset$ strings to be written.
|
||||
@ -2475,14 +2538,13 @@ def write_$group_dset$(trexio_file, dset_w: list) -> None:
|
||||
- Exception from some other error (e.g. RuntimeError).
|
||||
"""
|
||||
|
||||
|
||||
max_str_length = len(max(dset_w, key=len)) + 1
|
||||
|
||||
try:
|
||||
rc = trexio_write_$group_dset$(trexio_file, dset_w, max_str_length)
|
||||
rc = pytr.trexio_write_$group_dset$(trexio_file.pytrexio_s, dset_w, max_str_length)
|
||||
assert rc==TREXIO_SUCCESS
|
||||
except AssertionError:
|
||||
raise Exception(trexio_string_of_error(rc))
|
||||
raise Exception(pytr.trexio_string_of_error(rc))
|
||||
except:
|
||||
raise
|
||||
|
||||
@ -2495,7 +2557,7 @@ def read_$group_dset$(trexio_file, dim = None) -> list:
|
||||
Parameters:
|
||||
|
||||
trexio_file:
|
||||
TREXIO file handle.
|
||||
TREXIO File object.
|
||||
|
||||
dim (Optional): int
|
||||
Size of the block to be read from the file (i.e. how many items of $group_dset$ will be returned)
|
||||
@ -2510,7 +2572,6 @@ def read_$group_dset$(trexio_file, dim = None) -> list:
|
||||
- Exception from some other error (e.g. RuntimeError).
|
||||
"""
|
||||
|
||||
|
||||
# if dim is not specified, read dimensions from the TREXIO file
|
||||
if dim is None:
|
||||
$group_dset_dim$ = read_$group_dset_dim$(trexio_file)
|
||||
@ -2522,16 +2583,16 @@ def read_$group_dset$(trexio_file, dim = None) -> list:
|
||||
|
||||
|
||||
try:
|
||||
rc, dset_1d_r = trexio_read_$group_dset$_low(trexio_file, PYTREXIO_MAX_STR_LENGTH)
|
||||
rc, dset_1d_r = pytr.trexio_read_$group_dset$_low(trexio_file.pytrexio_s, PYTREXIO_MAX_STR_LENGTH)
|
||||
assert rc==TREXIO_SUCCESS
|
||||
except AssertionError:
|
||||
raise Exception(trexio_string_of_error(rc))
|
||||
raise Exception(pytr.trexio_string_of_error(rc))
|
||||
except:
|
||||
raise
|
||||
|
||||
|
||||
try:
|
||||
dset_full = dset_1d_r.split(TREXIO_DELIM)
|
||||
dset_full = dset_1d_r.split(pytr.TREXIO_DELIM)
|
||||
dset_2d_r = [dset_full[i] for i in range(dim) if dset_full[i]]
|
||||
assert dset_2d_r
|
||||
except AssertionError:
|
||||
@ -2726,7 +2787,7 @@ def write_$group_str$(trexio_file, str_w: str) -> None:
|
||||
Parameters:
|
||||
|
||||
trexio_file:
|
||||
TREXIO file handle.
|
||||
TREXIO File object.
|
||||
|
||||
str_w: str
|
||||
String corresponding to the $group_str$ variable to be written.
|
||||
@ -2736,14 +2797,13 @@ def write_$group_str$(trexio_file, str_w: str) -> None:
|
||||
- Exception from some other error (e.g. RuntimeError).
|
||||
"""
|
||||
|
||||
|
||||
max_str_length = len(str_w) + 1
|
||||
|
||||
try:
|
||||
rc = trexio_write_$group_str$(trexio_file, str_w, max_str_length)
|
||||
rc = pytr.trexio_write_$group_str$(trexio_file.pytrexio_s, str_w, max_str_length)
|
||||
assert rc==TREXIO_SUCCESS
|
||||
except AssertionError:
|
||||
raise Exception(trexio_string_of_error(rc))
|
||||
raise Exception(pytr.trexio_string_of_error(rc))
|
||||
except:
|
||||
raise
|
||||
#+end_src
|
||||
@ -2752,7 +2812,7 @@ def write_$group_str$(trexio_file, str_w: str) -> None:
|
||||
def read_$group_str$(trexio_file) -> str:
|
||||
"""Read the $group_str$ variable from the TREXIO file.
|
||||
|
||||
Parameter is a ~trexio_file~ object that has been created by a call to ~open~ function.
|
||||
Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
|
||||
|
||||
Returns:
|
||||
~str_r~: str
|
||||
@ -2763,12 +2823,11 @@ def read_$group_str$(trexio_file) -> str:
|
||||
- Exception from some other error (e.g. RuntimeError).
|
||||
"""
|
||||
|
||||
|
||||
try:
|
||||
rc, str_r = trexio_read_$group_str$(trexio_file, PYTREXIO_MAX_STR_LENGTH)
|
||||
rc, str_r = pytr.trexio_read_$group_str$(trexio_file.pytrexio_s, PYTREXIO_MAX_STR_LENGTH)
|
||||
assert rc==TREXIO_SUCCESS
|
||||
except AssertionError:
|
||||
raise Exception(trexio_string_of_error(rc))
|
||||
raise Exception(pytr.trexio_string_of_error(rc))
|
||||
except:
|
||||
raise
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user