mirror of
https://github.com/TREX-CoE/trexio.git
synced 2025-04-26 02:14:54 +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
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#=========================================================#
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# 0: TREXIO_HDF5 ; 1: TREXIO_TEXT
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TEST_TREXIO_BACKEND = tr.TREXIO_HDF5
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TEST_TREXIO_BACKEND = tr.TREXIO_TEXT
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OUTPUT_FILENAME_TEXT = 'test_py_swig.dir'
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OUTPUT_FILENAME_HDF5 = 'test_py_swig.h5'
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@ -37,7 +37,8 @@ except:
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#=========================================================#
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# create TREXIO file and open it for writing
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test_file = tr.open(output_filename, 'w', TEST_TREXIO_BACKEND)
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#test_file = tr.open(output_filename, 'w', TEST_TREXIO_BACKEND)
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test_file = tr.File(output_filename, mode='w', back_end=TEST_TREXIO_BACKEND)
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# Print docstring of the tr.open function
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#print(tr.open.__doc__)
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@ -107,15 +108,19 @@ labels = [
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tr.write_nucleus_label(test_file,labels)
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# close TREXIO file
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tr.close(test_file)
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# [TODO:] this functional call is no longer needed as we introduced TREXIO_File class which has a desctructor that closes the file
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#tr.close(test_file)
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# [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
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# 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)
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del test_file
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#==========================================================#
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#============ READ THE DATA FROM THE TEST FILE ============#
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#==========================================================#
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# open previously created TREXIO file, now in 'read' mode
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test_file2 = tr.open(output_filename, 'r', TEST_TREXIO_BACKEND)
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#test_file2 = tr.open(output_filename, 'r', TEST_TREXIO_BACKEND)
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test_file2 = tr.File(output_filename, 'r', TEST_TREXIO_BACKEND)
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# read nucleus_num from file
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rnum = tr.read_nucleus_num(test_file2)
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@ -164,7 +169,7 @@ rpoint_group = tr.read_nucleus_point_group(test_file2)
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assert rpoint_group==point_group
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# close TREXIO file
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tr.close(test_file2)
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#tr.close(test_file2)
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# cleaning (remove the TREXIO file)
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try:
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@ -92,7 +92,7 @@ Moreover, exception handling becomes trivial thanks to the use of TREXIO exit co
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try:
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from pytrexio.pytrexio import *
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import pytrexio.pytrexio as pytr
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except ImportError:
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raise Exception("Could not import pytrexio module from trexio package")
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@ -558,6 +558,76 @@ struct trexio_s {
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char padding[6]; /* Ensures the proper alignment of back ends */
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};
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#+end_src
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*** TREXIO_File Python class
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#+begin_src python :tangle basic_python.py
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class File:
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"""TREXIO File object.
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General information about the TREXIO file.
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Parameters:
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filename: str
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Is a name of the full path to the TREXIO file.
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back_end: int
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One of the currently supported TREXIO back ends.
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For example, TREXIO_HDF5 (0) or TREXIO_TEXT (1).
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mode: str
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One of the currently supported TREXIO open modes.
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For example, 'r' or 'w'.
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isOpen: bool
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Flag indicating whether the current object is still open for I/O
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pytrexio_s:
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A PyObject corresponding to SWIG proxy of the trexio_s struct in C.
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This argument is in fact a TREXIO file handle, which is required for
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communicating with the C back end.
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info: dict
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Dictionary of key-value pairs with additional information about the file.
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"""
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def __init__(self, filename, mode='r', back_end=TREXIO_HDF5,
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pytrexio_s=None, info=None):
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"""This is a TREXIO File constructor."""
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self.filename = filename
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self.mode = mode
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self.back_end = back_end
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self.isOpen = False
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if pytrexio_s is None:
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self.pytrexio_s = open(filename, mode, back_end)
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self.isOpen = True
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else:
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self.pytrexio_s = pytrexio_s
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self.isOpen = None
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self.info = info
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def close(self):
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"""Close a TREXIO File."""
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if self.isOpen:
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close(self.pytrexio_s)
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self.isOpen = False
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else:
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raise Exception("TREXIO File object has not been opened.")
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def __del__(self):
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"""This is a TREXIO File destructor."""
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if self.isOpen:
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close(self.pytrexio_s)
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elif self.isOpen is None:
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raise Exception("[WIP]: TREXIO file handle provided but what if the file is already closed?")
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else:
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pass
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#+end_src
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** Polymorphism of the file handle
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Polymorphism of the ~trexio_t~ type is handled by ensuring that the
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@ -767,7 +837,7 @@ end interface
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*** Python
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#+begin_src c :tangle basic_python.py
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#+begin_src python :tangle basic_python.py
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def open(file_name: str, mode: str, back_end: int):
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"""Create TREXIO file or open existing one.
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@ -790,9 +860,8 @@ def open(file_name: str, mode: str, back_end: int):
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>>> trex_file = tr_open("example.h5", "w", TREXIO_HDF5)
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"""
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try:
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trexio_file = trexio_open(file_name, mode, back_end)
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trexio_file = pytr.trexio_open(file_name, mode, back_end)
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assert trexio_file is not None
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except AssertionError:
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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.")
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@ -924,19 +993,18 @@ end interface
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*** Python
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#+begin_src c :tangle basic_python.py
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#+begin_src python :tangle basic_python.py
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def close(trexio_file):
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"""Close TREXIO file.
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Parameter is a ~trexio_file~ object that has been created by a call to ~open~ function.
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"""
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try:
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rc = trexio_close(trexio_file)
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rc = pytr.trexio_close(trexio_file)
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assert rc==TREXIO_SUCCESS
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except AssertionError:
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raise Exception(trexio_string_of_error(rc))
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raise Exception(pytr.trexio_string_of_error(rc))
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#+end_src
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* Templates for front end
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@ -1292,7 +1360,7 @@ def write_$group_num$(trexio_file, num_w: int) -> None:
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Parameters:
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trexio_file:
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TREXIO file handle.
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TREXIO File object.
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num_w: int
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Value of the $group_num$ variable to be written.
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@ -1302,12 +1370,11 @@ def write_$group_num$(trexio_file, num_w: int) -> None:
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- Exception from some other error (e.g. RuntimeError).
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"""
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try:
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rc = trexio_write_$group_num$(trexio_file, num_w)
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rc = pytr.trexio_write_$group_num$(trexio_file.pytrexio_s, num_w)
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assert rc==TREXIO_SUCCESS
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except AssertionError:
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raise Exception(trexio_string_of_error(rc))
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raise Exception(pytr.trexio_string_of_error(rc))
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except:
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raise
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@ -1317,7 +1384,7 @@ def write_$group_num$(trexio_file, num_w: int) -> None:
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def read_$group_num$(trexio_file) -> int:
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"""Read the $group_num$ variable from the TREXIO file.
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Parameter is a ~trexio_file~ object that has been created by a call to ~open~ function.
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Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
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Returns:
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~num_r~: int
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@ -1328,12 +1395,11 @@ def read_$group_num$(trexio_file) -> int:
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- Exception from some other error (e.g. RuntimeError).
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"""
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try:
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rc, num_r = trexio_read_$group_num$(trexio_file)
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rc, num_r = pytr.trexio_read_$group_num$(trexio_file.pytrexio_s)
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assert rc==TREXIO_SUCCESS
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except AssertionError:
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raise Exception(trexio_string_of_error(rc))
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raise Exception(pytr.trexio_string_of_error(rc))
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except:
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raise
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@ -1884,7 +1950,7 @@ def write_$group_dset$(trexio_file, dset_w) -> None:
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Parameters:
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trexio_file:
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TREXIO file handle.
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TREXIO File object.
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dset_w: list OR numpy.ndarray
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Array of $group_dset$ values to be written. If array data type does not correspond to int64 or float64, the conversion is performed.
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@ -1894,9 +1960,8 @@ def write_$group_dset$(trexio_file, dset_w) -> None:
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- Exception from some other error (e.g. RuntimeError).
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"""
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cutPrecision = False
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if not isinstance(dset_w, list):
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if not isinstance(dset_w, (list, tuple)):
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try:
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import numpy as np
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except ImportError:
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@ -1908,7 +1973,6 @@ def write_$group_dset$(trexio_file, dset_w) -> None:
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if cutPrecision:
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try:
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# TODO: we have to make sure that this conversion does not introduce any noise in the data.
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dset_64 = np.$group_dset_py_dtype$64(dset_w)
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except:
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raise
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@ -1916,13 +1980,13 @@ def write_$group_dset$(trexio_file, dset_w) -> None:
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try:
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if cutPrecision:
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rc = trexio_write_safe_$group_dset$_64(trexio_file, dset_64)
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rc = pytr.trexio_write_safe_$group_dset$_64(trexio_file.pytrexio_s, dset_64)
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else:
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rc = trexio_write_safe_$group_dset$_64(trexio_file, dset_w)
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rc = pytr.trexio_write_safe_$group_dset$_64(trexio_file.pytrexio_s, dset_w)
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assert rc==TREXIO_SUCCESS
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except AssertionError:
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raise Exception(trexio_string_of_error(rc))
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raise Exception(pytr.trexio_string_of_error(rc))
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except:
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raise
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@ -1935,7 +1999,7 @@ def read_$group_dset$(trexio_file, dim = None, dtype = None):
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Parameters:
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trexio_file:
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TREXIO file handle.
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TREXIO File object.
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dim (Optional): int
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Size of the block to be read from the file (i.e. how many items of $group_dset$ will be returned)
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@ -1952,7 +2016,6 @@ def read_$group_dset$(trexio_file, dim = None, dtype = None):
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- Exception from AssertionError if TREXIO return code ~rc~ is different from TREXIO_SUCCESS and prints the error message using trexio_string_of_error.
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- Exception from some other error (e.g. RuntimeError).
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"""
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# if dim is not specified, read dimensions from the TREXIO file
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if dim is None:
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@ -1965,10 +2028,10 @@ def read_$group_dset$(trexio_file, dim = None, dtype = None):
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try:
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rc, dset_64 = trexio_read_safe_$group_dset$_64(trexio_file, dim)
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rc, dset_64 = pytr.trexio_read_safe_$group_dset$_64(trexio_file.pytrexio_s, dim)
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assert rc==TREXIO_SUCCESS
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except AssertionError:
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raise Exception(trexio_string_of_error(rc))
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raise Exception(pytr.trexio_string_of_error(rc))
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except:
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raise
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@ -2465,7 +2528,7 @@ def write_$group_dset$(trexio_file, dset_w: list) -> None:
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Parameters:
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trexio_file:
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TREXIO file handle.
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TREXIO File object.
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dset_w: list
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Array of $group_dset$ strings to be written.
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@ -2475,14 +2538,13 @@ def write_$group_dset$(trexio_file, dset_w: list) -> None:
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- Exception from some other error (e.g. RuntimeError).
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"""
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max_str_length = len(max(dset_w, key=len)) + 1
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try:
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rc = trexio_write_$group_dset$(trexio_file, dset_w, max_str_length)
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rc = pytr.trexio_write_$group_dset$(trexio_file.pytrexio_s, dset_w, max_str_length)
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assert rc==TREXIO_SUCCESS
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except AssertionError:
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raise Exception(trexio_string_of_error(rc))
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raise Exception(pytr.trexio_string_of_error(rc))
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except:
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raise
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@ -2495,7 +2557,7 @@ def read_$group_dset$(trexio_file, dim = None) -> list:
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Parameters:
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trexio_file:
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TREXIO file handle.
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TREXIO File object.
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dim (Optional): int
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Size of the block to be read from the file (i.e. how many items of $group_dset$ will be returned)
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@ -2510,7 +2572,6 @@ def read_$group_dset$(trexio_file, dim = None) -> list:
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- Exception from some other error (e.g. RuntimeError).
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"""
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# if dim is not specified, read dimensions from the TREXIO file
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if dim is None:
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$group_dset_dim$ = read_$group_dset_dim$(trexio_file)
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@ -2522,16 +2583,16 @@ def read_$group_dset$(trexio_file, dim = None) -> list:
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try:
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rc, dset_1d_r = trexio_read_$group_dset$_low(trexio_file, PYTREXIO_MAX_STR_LENGTH)
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rc, dset_1d_r = pytr.trexio_read_$group_dset$_low(trexio_file.pytrexio_s, PYTREXIO_MAX_STR_LENGTH)
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assert rc==TREXIO_SUCCESS
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except AssertionError:
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raise Exception(trexio_string_of_error(rc))
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raise Exception(pytr.trexio_string_of_error(rc))
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except:
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raise
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try:
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dset_full = dset_1d_r.split(TREXIO_DELIM)
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dset_full = dset_1d_r.split(pytr.TREXIO_DELIM)
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dset_2d_r = [dset_full[i] for i in range(dim) if dset_full[i]]
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assert dset_2d_r
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except AssertionError:
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@ -2726,7 +2787,7 @@ def write_$group_str$(trexio_file, str_w: str) -> None:
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Parameters:
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trexio_file:
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TREXIO file handle.
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TREXIO File object.
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str_w: str
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String corresponding to the $group_str$ variable to be written.
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@ -2736,14 +2797,13 @@ def write_$group_str$(trexio_file, str_w: str) -> None:
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- Exception from some other error (e.g. RuntimeError).
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"""
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max_str_length = len(str_w) + 1
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try:
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rc = trexio_write_$group_str$(trexio_file, str_w, max_str_length)
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rc = pytr.trexio_write_$group_str$(trexio_file.pytrexio_s, str_w, max_str_length)
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assert rc==TREXIO_SUCCESS
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except AssertionError:
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raise Exception(trexio_string_of_error(rc))
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raise Exception(pytr.trexio_string_of_error(rc))
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except:
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raise
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#+end_src
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@ -2752,7 +2812,7 @@ def write_$group_str$(trexio_file, str_w: str) -> None:
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def read_$group_str$(trexio_file) -> str:
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"""Read the $group_str$ variable from the TREXIO file.
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Parameter is a ~trexio_file~ object that has been created by a call to ~open~ function.
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Parameter is a ~TREXIO File~ object that has been created by a call to ~open~ function.
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Returns:
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~str_r~: str
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@ -2763,12 +2823,11 @@ def read_$group_str$(trexio_file) -> str:
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- Exception from some other error (e.g. RuntimeError).
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"""
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try:
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rc, str_r = trexio_read_$group_str$(trexio_file, PYTREXIO_MAX_STR_LENGTH)
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rc, str_r = pytr.trexio_read_$group_str$(trexio_file.pytrexio_s, PYTREXIO_MAX_STR_LENGTH)
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assert rc==TREXIO_SUCCESS
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except AssertionError:
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raise Exception(trexio_string_of_error(rc))
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raise Exception(pytr.trexio_string_of_error(rc))
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except:
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raise
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