diff --git a/EStiMo_GUI_0123.py b/EStiMo_GUI.py
similarity index 99%
rename from EStiMo_GUI_0123.py
rename to EStiMo_GUI.py
index 6118651..90fe5bd 100644
--- a/EStiMo_GUI_0123.py
+++ b/EStiMo_GUI.py
@@ -5,8 +5,8 @@ Created on Tue Nov 23 11:11:41 2021
 
 @author: adamr
 """
-import NeurOne
-import RDA
+from connection import NeurOne, RDA
+# import RDA
 
 import time
 import matplotlib
@@ -21,16 +21,16 @@ import matplotlib.cm as cm
 import PyQt5.uic as uic
 import pandas as pd
 import json
-#import scipy.stats as st
+import scipy.stats as st
 import csv
 import datetime
 import ctypes
 import scipy 
 import pywt
-import queue
+# import queue
 
 from cycler import cycler
-from matplotlib.backend_bases import MouseButton
+# from matplotlib.backend_bases import MouseButton
 from PyQt5.QtCore import QTimer, Qt
 from PyQt5.QtGui import QImage, QPixmap, QIcon, QFont
 from PyQt5.QtWidgets import (QMainWindow, QFileDialog, QMessageBox, QCheckBox, QLineEdit, QWidget, QPushButton,
@@ -46,9 +46,9 @@ if sys.platform=='darwin':
     #from multiprocessing import Queue as QueueOld #Queue doesn't work on MacOS
 else:
     from multiprocessing import Process, Queue, Value
-from Waiting import Waiting_window
-from FirstWindow import First_window
-from Functions import (apply_montage, eye_reg, most_frequent, connect_sig, set_to_gray, update_stem, 
+from utils.Waiting import Waiting_window
+from utils.FirstWindow import First_window
+from utils.Functions import (apply_montage, eye_reg, most_frequent, connect_sig, set_to_gray, update_stem, 
                        adjust_hist, min_zero, pentropy, entropy, check_integrity, doubleMADsfromMedian)
         
 if sys.platform=='darwin':
@@ -215,7 +215,7 @@ def acquire_data(q, size, run, speed, downsample, sleep_time, ip = '192.168.200.
     run: Value class from multiprocessing library. That value can be changed in main process
     downsample: boolean value. Says if data will be downsampled to 1000 Hz
     sleep_time: int, set how often function should refresh. Usually it takes a bit more that that"""
-    # offline = 'offline'
+    offline = 'offline'
     #import NeurOne_v3
     if offline=="offline":
         NO = NeurOneOffline()
@@ -385,7 +385,7 @@ class AppForm(QMainWindow):
         
         #montage matrix is a matrix that is multiplied with the signal
         #identity matrix multiply all channels by 1, so we have the same signal as an output
-        settings_file = pd.read_csv('TMS_protocol.txt',sep=':', header=None) #read file with settings
+        settings_file = pd.read_csv('settings/TMS_protocol.txt',sep=':', header=None) #read file with settings
         print(restarted)
         #open the file to save values during the experiment
         self.log_file = open('logs//TMS_log_'+str(f"{datetime.datetime.now():%Y-%m-%d-%H-%M}"+restarted+'.csv'), 'w')
@@ -396,7 +396,7 @@ class AppForm(QMainWindow):
         self.size_of_up = 2*self.Fs #5000 how much data we get from NeurOne function
         
         #file with settings and assigning variables to them
-        settings_file = pd.read_csv('TMS_protocol.txt',sep=':', header=None)
+        # settings_file = pd.read_csv('settings/TMS_protocol.txt',sep=':', header=None)
         
         #params can be set in GUI, so then no need for using ones from the file
         if passed_params is not None:
@@ -470,7 +470,7 @@ class AppForm(QMainWindow):
         print(self.included_ch)
         # self.montage_matrix = np.identity(self.num_of_ch)
         if self.montage_file_path in [None, '']:
-            self.montage_file_path = 'montage_18ch.csv'
+            self.montage_file_path = 'settings/montage_18ch.csv'
         self.montage_matrix = np.array(pd.read_csv(self.montage_file_path, header=None))
         
             
@@ -743,7 +743,7 @@ class AppForm(QMainWindow):
             self.timer.setInterval(int(self.speed_general*1.03))
             
         times = time.time()
-        # self.offline='offline' #remove this!
+        self.offline='offline' #remove this!
         if self.offline=="offline":
             incl = [0,2,6,7,8,10,13,16,18,22,25,28,31,34,41,43,-3,-2,-1] # For offline only
             loaded_temp = self.q.get()[incl]/10 # Load data
@@ -1359,7 +1359,7 @@ class Ui(QMainWindow):
     def __init__(self, main_file):
         self.main_file = main_file
         super(Ui, self).__init__()
-        uic.loadUi('soft2.ui', self)
+        uic.loadUi('settings/soft2.ui', self)
         self.show()        
         self.load_button = self.findChild(QPushButton, 'pushButton')
         self.load_button.clicked.connect(self.get_file)
diff --git a/Electrode_selection.txt b/Electrode_selection.txt
deleted file mode 100644
index d23e13c..0000000
--- a/Electrode_selection.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-full_cap_file_path: /home/adamr/Documents/PYTHON/TMS TV/EStiMo/easycap-M10_63_NO.txt
-cap_file_path: /home/adamr/Documents/PYTHON/TMS TV/EStiMo/easycap-M10_16_NO.txt
diff --git a/NeurOne.py b/connection/NeurOne.py
similarity index 100%
rename from NeurOne.py
rename to connection/NeurOne.py
diff --git a/RDA.py b/connection/RDA.py
similarity index 100%
rename from RDA.py
rename to connection/RDA.py
diff --git a/connection/__init__.py b/connection/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/connection/__pycache__/NeurOne.cpython-38.pyc b/connection/__pycache__/NeurOne.cpython-38.pyc
new file mode 100644
index 0000000..ae586c6
Binary files /dev/null and b/connection/__pycache__/NeurOne.cpython-38.pyc differ
diff --git a/connection/__pycache__/RDA.cpython-38.pyc b/connection/__pycache__/RDA.cpython-38.pyc
new file mode 100644
index 0000000..1d7c382
Binary files /dev/null and b/connection/__pycache__/RDA.cpython-38.pyc differ
diff --git a/connection/__pycache__/__init__.cpython-38.pyc b/connection/__pycache__/__init__.cpython-38.pyc
new file mode 100644
index 0000000..494ef4b
Binary files /dev/null and b/connection/__pycache__/__init__.cpython-38.pyc differ
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..badee00
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,12 @@
+matplotlib==3.6.2
+mne==1.3.1
+numpy==1.23.5
+scipy==1.7.3
+pandas==2.0.0
+json==2.0.9
+csv
+datetime
+ctypes==1.1.0
+pywt==1.4.1
+cycler==0.10.0
+PyQt5
diff --git a/settings/Electrode_selection.txt b/settings/Electrode_selection.txt
new file mode 100644
index 0000000..2fe9b3b
--- /dev/null
+++ b/settings/Electrode_selection.txt
@@ -0,0 +1,2 @@
+full_cap_file_path: /home/adamr/Documents/PYTHON/TMS TV/EStiMo/settings/easycap-M10_63_NO.txt
+cap_file_path: /home/adamr/Documents/PYTHON/TMS TV/EStiMo/settings/easycap-M10_16_NO.txt
diff --git a/TMS_protocol.txt b/settings/TMS_protocol.txt
similarity index 100%
rename from TMS_protocol.txt
rename to settings/TMS_protocol.txt
diff --git a/easycap-M10_16_NO.txt b/settings/easycap-M10_16_NO.txt
similarity index 100%
rename from easycap-M10_16_NO.txt
rename to settings/easycap-M10_16_NO.txt
diff --git a/easycap-M10_63_NO.txt b/settings/easycap-M10_63_NO.txt
similarity index 100%
rename from easycap-M10_63_NO.txt
rename to settings/easycap-M10_63_NO.txt
diff --git a/montage_18ch.csv b/settings/montage_18ch.csv
similarity index 100%
rename from montage_18ch.csv
rename to settings/montage_18ch.csv
diff --git a/soft2.ui b/settings/soft2.ui
similarity index 100%
rename from soft2.ui
rename to settings/soft2.ui
diff --git a/FirstWindow.py b/utils/FirstWindow.py
similarity index 97%
rename from FirstWindow.py
rename to utils/FirstWindow.py
index 58c5ebe..75c124c 100644
--- a/FirstWindow.py
+++ b/utils/FirstWindow.py
@@ -6,6 +6,7 @@ Created on Mon Jan 24 11:26:23 2022
 """
 import mne
 import os, sys, traceback, time
+
 from PyQt5.QtWidgets import (QMainWindow, QFileDialog, QMessageBox, QCheckBox, QLineEdit, QWidget, QPushButton,
                              QLabel, QHBoxLayout, QGridLayout, QAction, QApplication, QDialog, QDialogButtonBox,
                              QVBoxLayout, QFrame, QTabWidget, QComboBox, QScrollArea, QFormLayout)
@@ -21,14 +22,13 @@ if sys.platform=='darwin':
     #from multiprocessing import Queue as StupidNotWorkingQueue
 else:
     from multiprocessing import Process, Queue, Value
-import NeurOne
-import RDA
-import ctypes
+from connection import NeurOne, RDA
 
 import pandas as pd
 from mne.channels.layout import _find_topomap_coords as get_pos
 import json
 import numpy as np
+import ctypes
 
 if sys.platform=='darwin':
     from multiprocessing.queues import Queue as QueueOld
@@ -225,15 +225,15 @@ class First_window(QMainWindow):
         self.setWindowTitle('EStiMo Configuration')
         
         try:
-            cap_loc_file = pd.read_csv('Electrode_selection.txt', sep=':', header=None)
+            cap_loc_file = pd.read_csv('settings/Electrode_selection.txt', sep=':', header=None)
             self.cap_file_path = cap_loc_file[cap_loc_file[0]=='cap_file_path'].values[0][1].strip()
             self.full_cap_file_path = cap_loc_file[cap_loc_file[0]=='full_cap_file_path'].values[0][1].strip() #'easycap-M10_63_NO.txt'
         except:
             print("CAP FILE EXCEPTION")
-            self.cap_file_path = 'easycap-M10_16_NO.txt'
-            self.full_cap_file_path = 'easycap-M10_63_NO.txt'
+            self.cap_file_path = 'settings/easycap-M10_16_NO.txt'
+            self.full_cap_file_path = 'settings/easycap-M10_63_NO.txt'
         
-        self.conf_path = 'TMS_protocol.txt'
+        self.conf_path = 'settings/TMS_protocol.txt'
         montage = mne.channels.read_custom_montage(self.cap_file_path)
         montage_file = pd.read_csv(self.cap_file_path, sep='\t')
         
diff --git a/Functions.py b/utils/Functions.py
similarity index 100%
rename from Functions.py
rename to utils/Functions.py
diff --git a/Waiting.py b/utils/Waiting.py
similarity index 100%
rename from Waiting.py
rename to utils/Waiting.py
diff --git a/utils/__init__.py b/utils/__init__.py
new file mode 100644
index 0000000..4b60ec9
--- /dev/null
+++ b/utils/__init__.py
@@ -0,0 +1,3 @@
+import sys, os
+# sys.path.append("..")
+sys.path.append(os.path.dirname(os.path.abspath(__file__))) 
diff --git a/utils/__pycache__/FirstWindow.cpython-38.pyc b/utils/__pycache__/FirstWindow.cpython-38.pyc
new file mode 100644
index 0000000..c2318e4
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diff --git a/utils/__pycache__/Functions.cpython-38.pyc b/utils/__pycache__/Functions.cpython-38.pyc
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index 0000000..d63512c
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diff --git a/utils/__pycache__/Waiting.cpython-38.pyc b/utils/__pycache__/Waiting.cpython-38.pyc
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index 0000000..8014d83
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diff --git a/utils/__pycache__/__init__.cpython-38.pyc b/utils/__pycache__/__init__.cpython-38.pyc
new file mode 100644
index 0000000..3873aa1
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diff --git a/features.py b/utils/features.py
similarity index 100%
rename from features.py
rename to utils/features.py