def calibrate_and_search(out_put_file_name, jobs):
import csv
ref_dict, cal_file_path = get_reference_dict()
if ref_dict:
file_dialog = QFileDialog()
file_dialog.setWindowFlags(Qt.WindowStaysOnTopHint)
if file_dialog:
file_locations = file_dialog.getOpenFileNames(
None, "Standard Compounds Files", filter="*.cdf")
file_dialog.close()
# run in multiprocessing mode
pool = Pool(jobs)
args = [(file_path, ref_dict, cal_file_path)
for file_path in file_locations[0]]
gcmss = pool.map(run, args)
pool.close()
pool.join()
for gcms in gcmss:
#gcms.to_csv(out_put_file_name, highest_score=False)
#gcms.to_excel(out_put_file_name, highest_score=False)
#gcms.to_pandas(out_put_file_name)
gcms.to_hdf(highest_score=False)
def get_reference_dict(calibration_file_path=False):
if not calibration_file_path:
app = QApplication(sys.argv)
file_dialog = QFileDialog()
file_dialog.setWindowFlags(Qt.WindowStaysOnTopHint)
file_path = file_dialog.getOpenFileName(None,
"FAMES REF FILE",
filter="*.cdf")[0]
file_dialog.close()
app.exit()
else:
file_path = calibration_file_path
if not file_path: return None
else:
gcms_ref_obj = get_gcms(file_path)
sql_obj = start_sql_from_file()
rt_ri_pairs = get_rt_ri_pairs(gcms_ref_obj, sql_obj=sql_obj)
# !!!!!! READ !!!!! use the previous two lines if db/pnnl_lowres_gcms_compounds.sqlite does not exist
# and comment the next line
#rt_ri_pairs = get_rt_ri_pairs(gcms_ref_obj)
return rt_ri_pairs, file_path
def calibrate_and_search(out_put_file_name, jobs):
from PySide2.QtWidgets import QFileDialog
from PySide2.QtCore import Qt
ref_dict, cal_file_path = get_reference_dict()
if ref_dict:
file_dialog = QFileDialog()
file_dialog.setWindowFlags(Qt.WindowStaysOnTopHint)
if file_dialog:
file_locations = file_dialog.getOpenFileNames(None, "Standard Compounds Files", filter="*.cdf")
file_dialog.close()
# run in multiprocessing mode
pool = Pool(jobs)
args = [(file_path, ref_dict, cal_file_path) for file_path in file_locations[0]]
gcmss = pool.map(run, args)
pool.close()
pool.join()
for file_index, gcms in enumerate(gcmss):
file_path = Path(file_locations[0][file_index])
# print(out_put_file_name)
gcms.to_csv(out_put_file_name, write_metadata=True, id_label="emsl:")
# gcms.to_excel(out_put_file_name)
# gcms.to_pandas(out_put_file_name)
gcms.to_hdf()
