def __init__(self, dir, printlabel, Settings="empty"):
from functions import fn_check_dir
from GUI_mainframe import update_GUI
update_GUI("Reading in experiment.", printlabel)
self.dir = dir
if Settings == "empty":
from functions import fn_settings
Settings = fn_settings()
self.Settings = Settings
self.printlabel = printlabel
if fn_check_dir(dir[:dir.find('pdata')], "pulseprogram"):
if "seldigpzs2d" in open(
dir[:dir.find('pdata')] + r"\pulseprogram",
"r").readlines()[0]:
self.pp = "seldigpzs2d"
self.init_seldigpzs2d(self.dir, self.printlabel)
elif "dipsigpphzs" in open(
dir[:dir.find('pdata')] + r"\pulseprogram",
"r").readlines()[0]:
self.pp = "dipsigpphzsbs"
self.init_dipsigpphzsbs(self.dir, self.printlabel)
else:
update_GUI("error; no correct pulseprogram found", printlabel)
def check_exp_status(self):
if type(self.experiment) == list:
from functions import fn_check_dir
if "pdata" in Settings["Experiment_Directory"] and fn_check_dir(Settings["Experiment_Directory"], "auditp.txt"):
self.change_exp_status("blue")
else:
self.change_exp_status("red")
else:
self.change_exp_status("green")
def check_data_status(self):
if type(self.database) == list:
from functions import fn_check_dir
status = fn_check_dir(Settings["Database_Directory"], "Database.p")
if status:
self.change_data_status("blue")
else:
self.change_data_status("red")
else:
if self.database.status:
self.change_data_status("green")
else:
self.change_data_status("orange")
def fn_load(self):
# load in the functions
from pickle import load
from functions import fn_check_dir
from GUI_mainframe import update_GUI
if (fn_check_dir(self.dir, r"\Database.p")):
self.content = load(open(self.dir + r"\Database.p", "rb"))
update_GUI("Loaded the Database from given location.",
self.printlabel)
self.fn_override_settings(self.Settings)
else:
self.content = []
update_GUI("No database file was found in the given location.",
self.printlabel)
return self
def fn_compile(self):
from GUI_mainframe import update_GUI
from functions import fn_check_folders
# check if database exist and prompt user
from functions import fn_check_dir, fn_progress_gen
if fn_check_dir(self.dir, "Database.p"):
import tkinter.messagebox as mg
if self.printlabel == "testing":
import tkinter as tk
crap = tk.Tk()
crap.withdraw()
override = mg.askyesno(
"Delete",
"Override current database?\nIf you are missing items the database will not be complete."
)
if not override:
update_GUI("Not performing database compilation.",
self.printlabel)
return
# check for all existing folders in the given location
dir_list = fn_check_folders(self.dir)
self.dir_list = dir_list
#initialise all experiments and calculate progressbar
progress = round(0.000000, 1)
update_GUI("Performing database compilation.", self.printlabel)
# wipe current
self.content = []
for y in range(len(self.dir_list)):
if round((1 + y) / (len(dir_list) + 1), 1) != progress:
progress = round(y / len(dir_list), 1)
update_GUI(fn_progress_gen(progress), self.printlabel)
#load in the experiment
exp = Experiment(dir_list[y] + "\\pdata\\1", "ignore")
for chunk in exp.chunks:
self.content.append(chunk)
self.status = self.fn_save()
def init_seldigpzs2d(self, dir, printlabel):
import nmrglue as ng
import numpy as np
from functions import fn_check_dir
from GUI_mainframe import update_GUI
self.dic, self.data = ng.bruker.read_pdata(dir)
# read in the alternate data if possible - compenation for the NMRGlue chunk error
# can be deleted once we fixed nmrglue!!!
if self.dic["procs"]["XDIM"] != self.dic["procs"]["FTSIZE"]:
self.data_file = ""
if fn_check_dir(dir, "DATABASE.txt"):
self.data_file = open(dir + r"\DATABASE.txt", 'r').readlines()
elif fn_check_dir(dir, "SAMPLES.txt"):
self.data_file = open(dir + r"\SAMPLES.txt", 'r').readlines()
if self.data_file != "":
self.data = []
for line in self.data_file:
if ("row" in line):
self.data.append([])
else:
if "#" not in line:
self.data[len(self.data) - 1].append(
float(line.replace(r"\n", "")))
else:
print("No extra data file was found...")
print("This was not correctly processed using topspin!")
quit()
# reform the data for oversaving effect
from copy import deepcopy
test_data = deepcopy(self.data)
self.data = []
for x in range(len(test_data)):
if (test_data[x][0] != 0.0):
self.data.append(test_data[x])
# collect the parameters
from functions import fn_vclist, fn_fqlist, fn_parameters, fn_read_title
self.dic2 = open(dir[:dir.find('pdata')] + r'\acqus', 'r').read()
self.dic3 = open(dir[:dir.find('pdata')] + r'\acqu2s', 'r').read()
self.B0_hz, self.SW_ppm, self.SW_hz, self.duplet_ppm, self.chunk_num, self.offset = fn_parameters(
self.dic, self.dic2, self.dic3, self.pp)
self.SW_ppm = 0.5 * self.SW_ppm
self.SO1_ppm = 0.5 * self.SW_ppm - self.offset
# collect the lists
self.vclist = fn_vclist(dir)
self.fqlist, self.fqlist_ppm = fn_fqlist(dir, self.B0_hz)
self.mtlist = np.array(self.vclist) * 115.112 * 25 * 10**(-6)
# colect the title
self.sample_name, self.extra_info, self.order = fn_read_title(dir)
# print out the title
update_GUI("Working on %s sample." % self.sample_name, self.printlabel)
# all data was read in now - end of initialisation of the sample
# starting the chunkification if present
import numpy as np
from functions import fn_unique
from GUI_mainframe import update_GUI
# find the unique fqs
self.fqlist_u = fn_unique(self.fqlist)
# chunk up the data per fq and remove the minus signals (reduce data amount for calculations)
self.chunks = []
update_GUI("Calculating peaks and integrals for each chunk.",
self.printlabel)
for x in range(self.chunk_num):
chunk = self.data[x * len(self.vclist):((x + 1) *
len(self.vclist))]
max = np.max(chunk)
row = chunk[0]
keep = int(len(row) / 2) # remove negative half
new_chunk, new_data = [], []
for row in chunk:
new_chunk.append(row[:keep] / max)
# create the title for the chunk
if len(self.order) != 0:
title = self.order[x]
else:
title = "%i-%s" % (x, self.sample_name)
#initialise chunk and perform the functions that are needed
chunk_temp = Chunk(new_chunk, title, self.fqlist[x], self.SW_ppm,
self.duplet_ppm, self.mtlist, self.SO1_ppm,
self.pp, self.printlabel, self.Settings)
self.chunks.append(chunk_temp)
#return self # list of all chunk objects
if self.Settings["plot_exp"]:
self.fn_plot()