def test_only_fid():
from cellpy.readers.core import FileID
my_fid_one = FileID()
my_file = fdv.cellpy_file_path
my_fid_one.populate(my_file)
my_fid_two = FileID(my_file)
assert my_fid_one.get_raw()[0] == my_fid_two.get_raw()[0]
assert my_fid_one.get_size() == my_fid_two.get_size()
def _init_data(self, file_name, global_data_df, test_no):
data = Cell()
data.cell_no = test_no
data.loaded_from = file_name
fid = FileID(file_name)
# name of the .res file it is loaded from:
# data.parent_filename = os.path.basename(file_name)
data.channel_index = int(
global_data_df[self.headers_global["channel_index_txt"]][test_no])
data.channel_number = int(
global_data_df[self.headers_global["channel_number_txt"]][test_no])
data.creator = global_data_df[
self.headers_global["creator_txt"]][test_no]
data.item_ID = global_data_df[
self.headers_global["item_id_txt"]][test_no]
data.schedule_file_name = global_data_df[
self.headers_global["schedule_file_name_txt"]][test_no]
data.start_datetime = global_data_df[
self.headers_global["start_datetime_txt"]][test_no]
data.test_ID = int(
global_data_df[self.headers_normal.test_id_txt][test_no])
data.test_name = global_data_df[
self.headers_global["test_name_txt"]][test_no]
data.raw_data_files.append(fid)
return data
def loader(self, file_name, *args, **kwargs):
"""Loads data into a DataSet object and returns it"""
new_tests = []
test_no = 1
channel_index = 1
channel_number = 1
creator = "no name"
item_ID = 1
schedule_file_name = "no name"
start_datetime = "2020.02.24 14:58:00"
test_ID = 1
test_name = "no name"
if not os.path.isfile(file_name):
self.logger.info("Missing file_\n %s" % file_name)
return None
self.logger.debug("in loader")
self.logger.debug("filename: %s" % file_name)
filesize = os.path.getsize(file_name)
hfilesize = humanize_bytes(filesize)
txt = "Filesize: %i (%s)" % (filesize, hfilesize)
self.logger.debug(txt)
data = Cell()
data.cell_no = test_no
data.loaded_from = file_name
fid = FileID(file_name)
data.channel_index = channel_index
data.channel_number = channel_number
data.creator = creator
data.item_ID = item_ID
data.schedule_file_name = schedule_file_name
data.start_datetime = start_datetime
data.test_ID = test_ID
data.test_name = test_name
data.raw_data_files.append(fid)
length_of_test, normal_df = load_nda()
data.summary = empty_df
data.raw = normal_df
data.raw_data_files_length.append(length_of_test)
data = self._post_process(data)
data = self.identify_last_data_point(data)
new_tests.append(data)
return new_tests
def loader(self, file_name, bad_steps=None, **kwargs):
new_tests = []
if not os.path.isfile(file_name):
self.logger.info("Missing file_\n %s" % file_name)
return None
filesize = os.path.getsize(file_name)
hfilesize = humanize_bytes(filesize)
txt = "Filesize: %i (%s)" % (filesize, hfilesize)
logging.debug(txt)
data = DataSet()
fid = FileID(file_name)
# div parameters and information (probably load this last)
test_no = 1
data.test_no = test_no
data.loaded_from = file_name
# some overall prms
data.channel_index = None
data.channel_number = None
data.creator = None
data.item_ID = None
data.schedule_file_name = None
data.test_ID = None
data.test_name = None
data.raw_data_files.append(fid)
# --------- read raw-data (normal-data) -------------------------
self._load_pec_data(file_name, bad_steps)
data.start_datetime = self.pec_settings["start_time"]
length_of_test = self.pec_data.shape[0]
logging.debug(f"length of test: {length_of_test}")
logging.debug("renaming columns")
self._rename_headers()
self._convert_units()
data.dfdata = self.pec_data
data.raw_data_files_length.append(length_of_test)
new_tests.append(data)
return new_tests
def loader(self, file_name, bad_steps=None, **kwargs):
"""Loads data from biologics .mpr files.
Args:
file_name (str): path to .res file.
bad_steps (list of tuples): (c, s) tuples of steps s
(in cycle c) to skip loading.
Returns:
new_tests (list of data objects)
"""
new_tests = []
if not os.path.isfile(file_name):
self.logger.info("Missing file_\n %s" % file_name)
return None
filesize = os.path.getsize(file_name)
hfilesize = humanize_bytes(filesize)
txt = "Filesize: %i (%s)" % (filesize, hfilesize)
self.logger.debug(txt)
# creating temporary file and connection
temp_dir = tempfile.gettempdir()
temp_filename = os.path.join(temp_dir, os.path.basename(file_name))
shutil.copy2(file_name, temp_dir)
self.logger.debug("tmp file: %s" % temp_filename)
self.logger.debug("HERE WE LOAD THE DATA")
data = DataSet()
fid = FileID(file_name)
# div parameters and information (probably load this last)
test_no = 1
data.test_no = test_no
data.loaded_from = file_name
# some overall prms
data.channel_index = None
data.channel_number = None
data.creator = None
data.item_ID = None
data.schedule_file_name = None
data.start_datetime = None
data.test_ID = None
data.test_name = None
data.raw_data_files.append(fid)
# --------- read raw-data (normal-data) -------------------------
self.logger.debug("reading raw-data")
self.mpr_data = None
self.mpr_log = None
self.mpr_settings = None
self._load_mpr_data(temp_filename, bad_steps)
length_of_test = self.mpr_data.shape[0]
self.logger.debug(f"length of test: {length_of_test}")
self.logger.debug("renaming columns")
self._rename_headers()
# --------- stats-data (summary-data) -------------------------
summary_df = self._create_summary_data()
if summary_df.empty:
txt = "\nCould not find any summary (stats-file)!"
txt += " (summary_df.empty = True)"
txt += "\n -> issue make_summary(use_cellpy_stat_file=False)"
warnings.warn(txt)
data.dfsummary = summary_df
data.dfdata = self.mpr_data
data.raw_data_files_length.append(length_of_test)
new_tests.append(data)
self._clean_up(temp_filename)
return new_tests
def _generate_fid(self, file_name, var_dict):
fid = FileID()
last_modified = var_dict.get(
self.variables["fid_last_modification_time"],
None,
)
size = var_dict.get(
self.variables["fid_size"],
None,
)
last_accessed = var_dict.get(
self.variables["fid_last_accessed"],
None,
)
if any([last_modified, size, last_accessed]):
fid.name = os.path.abspath(file_name)
fid.full_name = file_name
fid.location = os.path.dirname(file_name)
fid.size = size
fid.last_modified = last_modified
fid.last_accessed = last_accessed
fid.last_info_changed = last_accessed
else:
fid.populate(file_name)
return fid
def loader(self, file_name, bad_steps=None, **kwargs):
"""Loads data from arbin .res files.
Args:
file_name (str): path to .res file.
bad_steps (list of tuples): (c, s) tuples of steps s (in cycle c)
to skip loading.
Returns:
new_tests (list of data objects)
"""
# TODO: @jepe - insert kwargs - current chunk, only normal data, etc
if DEBUG_MODE:
time_0 = time.time()
new_tests = []
if not os.path.isfile(file_name):
self.logger.info("Missing file_\n %s" % file_name)
return None
self.logger.debug("in loader")
self.logger.debug("filename: %s" % file_name)
filesize = os.path.getsize(file_name)
hfilesize = humanize_bytes(filesize)
txt = "Filesize: %i (%s)" % (filesize, hfilesize)
self.logger.debug(txt)
if (filesize > prms.Instruments.Arbin.max_res_filesize
and not prms.Reader.load_only_summary):
error_message = "\nERROR (loader):\n"
error_message += "%s > %s - File is too big!\n" % (
hfilesize,
humanize_bytes(prms.Instruments.Arbin.max_res_filesize),
)
error_message += "(edit prms.Instruments.Arbin" "['max_res_filesize'])\n"
print(error_message)
return None
table_name_global = TABLE_NAMES["global"]
table_name_stats = TABLE_NAMES["statistic"]
table_name_normal = TABLE_NAMES["normal"]
# creating temporary file and connection
temp_dir = tempfile.gettempdir()
temp_filename = os.path.join(temp_dir, os.path.basename(file_name))
shutil.copy2(file_name, temp_dir)
self.logger.debug("tmp file: %s" % temp_filename)
use_mdbtools = False
if use_subprocess:
use_mdbtools = True
if is_posix:
use_mdbtools = True
# windows with same python bit as windows bit (the ideal case)
if not use_mdbtools:
constr = self.__get_res_connector(temp_filename)
if use_ado:
conn = dbloader.connect(constr)
else:
conn = dbloader.connect(constr, autocommit=True)
self.logger.debug("constr str: %s" % constr)
self.logger.debug("reading global data table")
sql = "select * from %s" % table_name_global
self.logger.debug("sql statement: %s" % sql)
global_data_df = pd.read_sql_query(sql, conn)
# col_names = list(global_data_df.columns.values)
else:
import subprocess
if is_posix:
if is_macos:
self.logger.debug("\nMAC OSX USING MDBTOOLS")
else:
self.logger.debug("\nPOSIX USING MDBTOOLS")
else:
self.logger.debug("\nWINDOWS USING MDBTOOLS-WIN")
# creating tmp-filenames
temp_csv_filename_global = os.path.join(temp_dir, "global_tmp.csv")
temp_csv_filename_normal = os.path.join(temp_dir, "normal_tmp.csv")
temp_csv_filename_stats = os.path.join(temp_dir, "stats_tmp.csv")
# making the cmds
mdb_prms = [
(table_name_global, temp_csv_filename_global),
(table_name_normal, temp_csv_filename_normal),
(table_name_stats, temp_csv_filename_stats),
]
# executing cmds
for table_name, tmp_file in mdb_prms:
with open(tmp_file, "w") as f:
subprocess.call(
[sub_process_path, temp_filename, table_name],
stdout=f)
self.logger.debug(f"ran mdb-export {str(f)} {table_name}")
# use pandas to load in the data
global_data_df = pd.read_csv(temp_csv_filename_global)
tests = global_data_df[self.headers_normal.test_id_txt]
number_of_sets = len(tests)
self.logger.debug("number of datasets: %i" % number_of_sets)
for counter, test_no in enumerate(range(number_of_sets)):
if counter > 0:
self.logger.warning("***MULTITEST-FILE (not recommended)")
if not ALLOW_MULTI_TEST_FILE:
break
data = Cell()
data.cell_no = test_no
data.loaded_from = file_name
fid = FileID(file_name)
# name of the .res file it is loaded from:
# data.parent_filename = os.path.basename(file_name)
data.channel_index = int(global_data_df[
self.headers_global["channel_index_txt"]][test_no])
data.channel_number = int(global_data_df[
self.headers_global["channel_number_txt"]][test_no])
data.creator = global_data_df[
self.headers_global["creator_txt"]][test_no]
data.item_ID = global_data_df[
self.headers_global["item_id_txt"]][test_no]
data.schedule_file_name = global_data_df[
self.headers_global["schedule_file_name_txt"]][test_no]
data.start_datetime = global_data_df[
self.headers_global["start_datetime_txt"]][test_no]
data.test_ID = int(
global_data_df[self.headers_normal.test_id_txt][test_no])
data.test_name = global_data_df[
self.headers_global["test_name_txt"]][test_no]
data.raw_data_files.append(fid)
self.logger.debug("reading raw-data")
if not use_mdbtools:
# --------- read raw-data (normal-data) ------------------------
length_of_test, normal_df = self._load_res_normal_table(
conn, data.test_ID, bad_steps)
# --------- read stats-data (summary-data) ---------------------
sql = "select * from %s where %s=%s order by %s" % (
table_name_stats,
self.headers_normal.test_id_txt,
data.test_ID,
self.headers_normal.data_point_txt,
)
summary_df = pd.read_sql_query(sql, conn)
if counter > number_of_sets:
self._clean_up_loadres(None, conn, temp_filename)
else:
normal_df = pd.read_csv(temp_csv_filename_normal)
# filter on test ID
normal_df = normal_df[normal_df[
self.headers_normal.test_id_txt] == data.test_ID]
# sort on data point
if prms._sort_if_subprocess:
normal_df = normal_df.sort_values(
self.headers_normal.data_point_txt)
length_of_test = normal_df.shape[0]
summary_df = pd.read_csv(temp_csv_filename_stats)
# clean up
for f in [
temp_filename,
temp_csv_filename_stats,
temp_csv_filename_normal,
temp_csv_filename_global,
]:
if os.path.isfile(f):
try:
os.remove(f)
except WindowsError as e:
self.logger.warning(
f"could not remove tmp-file\n{f} {e}")
if summary_df.empty and prms.Reader.use_cellpy_stat_file:
txt = "\nCould not find any summary (stats-file)!"
txt += "\n -> issue make_summary(use_cellpy_stat_file=False)"
logging.debug(txt)
# normal_df = normal_df.set_index("Data_Point")
data.summary = summary_df
if DEBUG_MODE:
mem_usage = normal_df.memory_usage()
logging.debug(f"memory usage for "
f"loaded data: \n{mem_usage}"
f"\ntotal: {humanize_bytes(mem_usage.sum())}")
logging.debug(f"time used: {(time.time() - time_0):2.4f} s")
data.raw = normal_df
data.raw_data_files_length.append(length_of_test)
data = self._post_process(data)
new_tests.append(data)
new_tests = self._inspect(new_tests)
return new_tests