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Added an extra entry widget to set the upper boundary for the single stranded contour length.
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@Gundura
Gundura authored Mar 9, 2023
1 parent 6617e7d commit 17bb81b
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Showing 3 changed files with 83 additions and 104 deletions.
161 changes: 73 additions & 88 deletions POTATO_GUI.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
"""Copyright 2021 Helmholtz-Zentrum für Infektionsforschung GmbH"""

""" POTATO -- 2021-10-14 -- Version 1.1
""" POTATO -- 2022-12-13 -- Version 1.6
Developed by Lukáš Pekárek and Stefan Buck at the Helmholtz Institute for RNA-based Infection Research
In the research group REMI - Recoding Mechanisms in Infections
Supervisor - Jun. Prof. Neva Caliskan """
Expand All @@ -21,7 +21,6 @@
import pandas as pd
import numpy as np
import os
import h5py
import glob
import time
import multiprocessing as mp
Expand Down Expand Up @@ -125,11 +124,14 @@ def parameters(default_values, default_fit, default_constantF):
dsLp_low_variable.set(str(default_fit['Persistance-Length ds, lower bound, nm']))
ssLp_variable.set(str(default_fit['Persistance-Length ss, nm']))
dsLc_variable.set(str(default_fit['Contour-Length ds, nm']))
ssLc_variable.set(str(default_fit['Persistance-Length ss, nm']))
ssLc_variable.set(str(default_fit['Contour-Length ss, nm']))
ssLc_up_variable.set(str(default_fit['Contour-Length ss, upper bound, nm']))
stiff_ds_variable.set(str(default_fit['Stiffness ds, pN']))
stiff_ds_up_variable.set(str(default_fit['Stiffness ds, upper bound, pN']))
stiff_ds_low_variable.set(str(default_fit['Stiffness ds, lower bound, pN']))
stiff_ss_variable.set(str(default_fit['Stiffness ss, pN']))
stiff_ss_up_variable.set(str(default_fit['Stiffness ss, upper bound, pN']))
stiff_ss_low_variable.set(str(default_fit['Stiffness ss, lower bound, pN']))
f_off_variable.set(str(default_fit['Force offset, pN']))
f_off_up_variable.set(str(default_fit['Force offset, upper bound, pN']))
f_off_low_variable.set(str(default_fit['Force offset, lower bound, pN']))
Expand Down Expand Up @@ -197,10 +199,13 @@ def check_settings():
'lc_ds': float(dsLc.get()),
'lp_ss': float(ssLp.get()),
'lc_ss': float(ssLc.get()),
'lc_ss_up': float(ssLc_up.get()),
'ds_stiff': float(stiff_ds.get()),
'ds_stiff_up': float(stiff_ds_up.get()),
'ds_stiff_low': float(stiff_ds_low.get()),
'ss_stiff': float(stiff_ss.get()),
'ss_stiff_up': float(stiff_ss_up.get()),
'ss_stiff_low': float(stiff_ss_low.get()),
'offset_f': float(f_off.get()),
'offset_f_up': float(f_off_up.get()),
'offset_f_low': float(f_off_low.get()),
Expand All @@ -223,6 +228,7 @@ def check_settings():
return input_settings, input_format, export_data, input_fitting, input_constantF


# export parameters used for the analysis in a txt file
def export_settings(analysis_path, timestamp, input_1, input_2):
with open(str(analysis_path + '/parameters_' + timestamp + '.txt'), 'w') as config_used:
config_used.write('Data processing:\n')
Expand All @@ -234,7 +240,6 @@ def export_settings(analysis_path, timestamp, input_1, input_2):

# Looks for output of the subprocess
def refresh():
global new_image
while output_q.empty() is False:
output = output_q.get()
output_window.insert("end", "\n" + output + "\n")
Expand All @@ -260,65 +265,34 @@ def readme():
text.insert("end", help_text)


# display a single h5 file (tab2)
def getRAW_File_h5():
input_settings, input_format, export_data, input_fitting, input_constantF = check_settings()
import_file_path = filedialog.askopenfilename()
with h5py.File(import_file_path, "r") as raw_data:
# access the raw data
if input_format['HF'] == 1:
if input_format['Trap'] == 1:
Force = raw_data.get("Force HF/Force 1x")
elif input_format['Trap'] == 0:
Force = raw_data.get("Force HF/Force 2x")
Distance = raw_data.get("Distance/Piezo Distance")

elif input_format['LF'] == 1:
if input_format['Trap'] == 1:
load_force = raw_data.get("Force LF/Force 1x")
Force = load_force[:]['Value'][:]
load_distance = raw_data.get("Distance/Distance 1x")[:]
Distance = load_distance['Value'][:]
elif input_format['Trap'] == 0:
load_force = raw_data.get("Force LF/Force 2x")
Force = load_force[:]['Value'][:]
load_distance = raw_data.get("Distance/Distance 2x")[:]
Distance = load_distance['Value'][:]
if input_format['preprocess'] == 1:
FD, FD_um = preprocess_RAW(Force, Distance, input_settings)
display_RAW_FD(FD[:, 0], FD[:, 1], Force[::input_settings['downsample_value']], Distance[::input_settings['downsample_value']] * 1000)
# display a single file (tab2)
def get_single_file(format):
if format == 'csv':
if not check_box_CSV.get() == 1:
check_box_CSV.set(value=1)
select_box(check_box_CSV, check_box_HF, check_box_LF)
parameters(default_values_CSV, default_values_FIT, default_values_constantF)
else:
Force = np.array(Force)
Distance = np.array(Distance)
display_RAW_FD(Force, Distance, Force, Distance)


# display a single csv file (tab2)
def getRAW_File_csv():
if not check_box_CSV.get() == 1:
check_box_CSV.set(value=1)
select_box(check_box_CSV, check_box_HF, check_box_LF)
parameters(default_values_CSV, default_values_FIT, default_values_constantF)
else:
pass
pass

input_settings, input_format, export_data, input_fitting, input_constantF = check_settings()
import_file_path = filedialog.askopenfilename()
input_format['preprocess'] = 0
FD_raw, FD_raw_um, Frequency_value, filename = read_in_data(0, [import_file_path], input_settings, input_format)
input_format['preprocess'] = 1
FD, FD_um, Frequency_value, filename = read_in_data(0, [import_file_path], input_settings, input_format)
display_RAW_FD(FD[:, 0], FD[:, 1], FD_raw[:, 0], FD_raw[:, 1], filename)

df = pd.read_csv(import_file_path)

Force = df.to_numpy()[:, 0]
Distance = df.to_numpy()[:, 1]

if input_format['preprocess'] == 1:
FD, FD_um = preprocess_RAW(Force, Distance, input_settings)
display_RAW_FD(FD[:, 0], FD[:, 1], Force[::input_settings['downsample_value']], Distance[::input_settings['downsample_value']] * 1000)
else:
display_RAW_FD(Force, Distance, Force, Distance)
# create the plot for tab2
def display_RAW_FD(processed_F, processed_D, raw_F, raw_D, filename):
global figure_raw

try:
figure_raw.get_tk_widget().destroy()
except:
pass

# create the plot for tab2
def display_RAW_FD(processed_F, processed_D, raw_F, raw_D):
single_fd = Figure(figsize=(10, 6), dpi=100)
subplot1 = single_fd.add_subplot(111)

Expand All @@ -327,6 +301,7 @@ def display_RAW_FD(processed_F, processed_D, raw_F, raw_D):
Line2D([0], [0], color='C1', lw=4)
]

subplot1.set_title(str(filename))
subplot1.set_xlabel("Distance (nm)")
subplot1.set_ylabel("Force (pN)")
subplot1.plot(raw_D, raw_F, alpha=0.8, color='C0', zorder=0)
Expand Down Expand Up @@ -772,28 +747,26 @@ def export_table():
for child in tree_results.get_children():
results.append(tree_results.item(child)['values'])

Fit_results = pd.DataFrame(results,
columns=[
'Filename',
'step number',
'Force step start [pN]',
'Force step end [pN]',
'mean force [pN]',
'extension step start [nm]',
'extension step end [nm]',
'Step length [nm]',
'ds contour length',
'ds persistance Length',
'ds stiffness (K0) [pN]',
'ss contour Length',
'ss persistance Length',
'ss stiffness (K0) [pN]',
'Force offset',
'Distance offset',
'Work [pN*nm]',
'Work [kT]'
]
)
Fit_results = pd.DataFrame(results, columns=[
'Filename',
'step number',
'Force step start [pN]',
'Force step end [pN]',
'mean force [pN]',
'extension step start [nm]',
'extension step end [nm]',
'Step length [nm]',
'ds contour length',
'ds persistance Length',
'ds stiffness (K0) [pN]',
'ss contour Length',
'ss persistance Length',
'ss stiffness (K0) [pN]',
'Force offset',
'Distance offset',
'Work [pN*nm]',
'Work [kT]'
])

name = filedialog.asksaveasfile(mode='w', defaultextension=".csv")
Fit_results.to_csv(name.name, index=False, header=True)
Expand Down Expand Up @@ -837,8 +810,8 @@ def tab_bind(event=None):
file_menu = tk.Menu(drop_down_menu, tearoff=0)
drop_down_menu.add_cascade(label='File', menu=file_menu)
file_menu.add_command(label='Analyse folder (FD curves)', command=start_analysis)
file_menu.add_command(label='Display single FD curve (h5)', command=getRAW_File_h5)
file_menu.add_command(label='Display single FD curve (csv)', command=getRAW_File_csv)
file_menu.add_command(label='Display single FD curve (h5)', command=lambda: get_single_file('h5'))
file_menu.add_command(label='Display single FD curve (csv)', command=lambda: get_single_file('csv'))
file_menu.add_separator()
file_menu.add_command(label='Display constant force', command=show_constantF)
file_menu.add_command(label='Fit constant force', command=start_constantF)
Expand All @@ -863,12 +836,6 @@ def tab_bind(event=None):
tab4 = ttk.Frame(tabControl, width=800, height=600)
tab5 = ttk.Frame(tabControl, width=800, height=600)

tab1.grid(row=0, column=0, padx=2, pady=2)
tab2.grid(row=0, column=0, padx=2, pady=2)
tab3.grid(row=0, column=0, padx=2, pady=2)
tab4.grid(row=0, column=0, padx=2, pady=2)
tab5.grid(row=0, column=0, padx=2, pady=2)

# ATTENTION - tab3 and tab4 are displayed the other way round in the GUI
tabControl.add(tab1, text="Folder Analysis")
tabControl.add(tab2, text="Show Single File")
Expand Down Expand Up @@ -1066,7 +1033,7 @@ def select_box(*check_box):
BUTTON2 = tk.Button(
parameter_frame2,
text='Open h5 file',
command=getRAW_File_h5,
command=lambda: get_single_file('h5'),
bg='#df4c4c',
activebackground='#eaa90d',
font='Helvetica 11 bold',
Expand All @@ -1079,7 +1046,7 @@ def select_box(*check_box):
BUTTON3 = tk.Button(
parameter_frame2,
text='Open csv file',
command=getRAW_File_csv,
command=lambda: get_single_file('csv'),
bg='#df4c4c',
activebackground='#eaa90d',
font='Helvetica 11 bold',
Expand All @@ -1089,7 +1056,7 @@ def select_box(*check_box):

BUTTON3.grid(row=1, column=0, pady=20, sticky='E')

"""organize tab3 """
"""organize tab3 - advanced settings """
frame1 = tk.Frame(tab3, borderwidth=1, relief='ridge')
frame1.grid(row=0, column=0, sticky='N')
frame2 = tk.Frame(tab3, borderwidth=1, relief='ridge')
Expand Down Expand Up @@ -1216,10 +1183,13 @@ def select_box(*check_box):
Label_dsLc = tk.Label(frame3, text='dsLc [nm]')
Label_ssLp = tk.Label(frame3, text='ssLp [nm]')
Label_ssLc = tk.Label(frame3, text='ssLc [nm]')
Label_ssLc_up = tk.Label(frame3, text='ssLc upper bound [nm]')
Label_stiffness_ds = tk.Label(frame3, text='dsK0 [pN]')
Label_stiffness_ds_up = tk.Label(frame3, text='dsK0 upper bound [pN]')
Label_stiffness_ds_low = tk.Label(frame3, text='dsK0 lower bound [pN]')
Label_stiffness_ss = tk.Label(frame3, text='ssK0 [pN]')
Label_stiffness_ss_up = tk.Label(frame3, text='ssK0 upper bound [pN]')
Label_stiffness_ss_low = tk.Label(frame3, text='ssK0 lower bound [pN]')
Label_f_offset = tk.Label(frame3, text='Force offset [pN]')
Label_f_offset_up = tk.Label(frame3, text='Force offset upper bound [pN]')
Label_f_offset_low = tk.Label(frame3, text='Force offset lower bound [pN]')
Expand All @@ -1240,6 +1210,8 @@ def select_box(*check_box):
ssLp = tk.Entry(frame3, textvariable=ssLp_variable)
ssLc_variable = tk.StringVar()
ssLc = tk.Entry(frame3, textvariable=ssLc_variable)
ssLc_up_variable = tk.StringVar()
ssLc_up = tk.Entry(frame3, textvariable=ssLc_up_variable)
stiff_ds_variable = tk.StringVar()
stiff_ds = tk.Entry(frame3, textvariable=stiff_ds_variable)
stiff_ds_up_variable = tk.StringVar()
Expand All @@ -1248,6 +1220,10 @@ def select_box(*check_box):
stiff_ds_low = tk.Entry(frame3, textvariable=stiff_ds_low_variable)
stiff_ss_variable = tk.StringVar()
stiff_ss = tk.Entry(frame3, textvariable=stiff_ss_variable)
stiff_ss_up_variable = tk.StringVar()
stiff_ss_up = tk.Entry(frame3, textvariable=stiff_ss_up_variable)
stiff_ss_low_variable = tk.StringVar()
stiff_ss_low = tk.Entry(frame3, textvariable=stiff_ss_low_variable)
f_off_variable = tk.StringVar()
f_off = tk.Entry(frame3, textvariable=f_off_variable)
f_off_up_variable = tk.StringVar()
Expand Down Expand Up @@ -1295,6 +1271,9 @@ def select_box(*check_box):
Label_ssLc.grid(row=3, column=2, sticky=tk.E + tk.W, padx=2, pady=2)
ssLc.grid(row=3, column=3, padx=(0, 20), pady=2)

Label_ssLc_up.grid(row=4, column=2, sticky=tk.E + tk.W, padx=2, pady=2)
ssLc_up.grid(row=4, column=3, padx=(0, 20), pady=2)

Label_stiffness_ds.grid(row=6, column=0, sticky=tk.E + tk.W, padx=2, pady=2)
stiff_ds.grid(row=6, column=1, padx=(0, 20), pady=2)

Expand All @@ -1307,6 +1286,12 @@ def select_box(*check_box):
Label_stiffness_ss.grid(row=6, column=2, sticky=tk.E + tk.W, padx=2, pady=2)
stiff_ss.grid(row=6, column=3, padx=(0, 20), pady=2)

Label_stiffness_ss_up.grid(row=7, column=2, sticky=tk.E + tk.W, padx=2, pady=2)
stiff_ss_up.grid(row=7, column=3, padx=(0, 20), pady=2)

Label_stiffness_ss_low.grid(row=8, column=2, sticky=tk.E + tk.W, padx=2, pady=2)
stiff_ss_low.grid(row=8, column=3, padx=(0, 20), pady=2)

Label_f_offset.grid(row=9, column=0, sticky=tk.E + tk.W, padx=2, pady=2)
f_off.grid(row=9, column=1, padx=(0, 20), pady=2)

Expand Down
7 changes: 5 additions & 2 deletions POTATO_config.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -46,12 +46,15 @@
'Persistance-Length ds, upper bound, nm': '80',
'Persistance-Length ds, lower bound, nm': '12',
'Persistance-Length ss, nm': '1',
'Contour-Length ds, nm': '1250',
'Contour-Length ss, nm': '0',
'Contour-Length ds, nm': '1261',
'Contour-Length ss, nm': '1',
'Contour-Length ss, upper bound, nm': '500',
'Stiffness ds, pN': '500',
'Stiffness ds, upper bound, pN': '600',
'Stiffness ds, lower bound, pN': '400',
'Stiffness ss, pN': '800',
'Stiffness ss, upper bound, pN': '1500',
'Stiffness ss, lower bound, pN': '300',
'Force offset, pN': '0',
'Force offset, upper bound, pN': '3',
'Force offset, lower bound, pN': '-3',
Expand Down
19 changes: 5 additions & 14 deletions POTATO_fitting.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,8 @@
"""define the functions used for fitting"""


# if the step start/end are selected manually by TOMATO,
# the nearest point on the curve is selected in the array
def find_nearest(array, value):
array = np.asarray(array)
idx = (np.abs(array - value)).argmin()
Expand All @@ -34,17 +36,6 @@ def fitting_ds(filename_i, input_settings, export_data, input_fitting, i_start,
f_fitting_region_ds = Force_Distance[0:start_step1, 0]
d_fitting_region_ds = Force_Distance[0:start_step1, 1]

# start_step1 = start_step1[0][0]

# delta_f = f_fitting_region_ds[-1] - f_fitting_region_ds[0]
# delta_d = d_fitting_region_ds[-1] - d_fitting_region_ds[0]
# d_f_ratio = delta_d / delta_f
#
# # downsample the data used for fitting with a dD/dF ratio
# while len(f_fitting_region_ds) > 100 * d_f_ratio:
# f_fitting_region_ds = f_fitting_region_ds[::2]
# d_fitting_region_ds = d_fitting_region_ds[::2]

model_ds = lk.inverted_odijk("ds_part").subtract_independent_offset() + lk.force_offset("ds_part")

fit_ds = lk.FdFit(model_ds)
Expand Down Expand Up @@ -188,13 +179,13 @@ def fitting_ss(filename_i, input_settings, export_data, input_fitting, i_start,

# stiffnes
fit_ss["RNA/St"].value = input_fitting['ss_stiff']
fit_ss["RNA/St"].lower_bound = 300
fit_ss["RNA/St"].upper_bound = 1500
fit_ss["RNA/St"].lower_bound = input_fitting['ss_stiff_low']
fit_ss["RNA/St"].upper_bound = input_fitting['ss_stiff_up']

# contour length
fit_ss["RNA/Lc"].value = input_fitting['lc_ss']
fit_ss["RNA/Lc"].lower_bound = 0
fit_ss["RNA/Lc"].upper_bound = input_fitting['lc_ss'] + 100
fit_ss["RNA/Lc"].upper_bound = input_fitting['lc_ss_up']

fit_ss["RNA/Lc"].unit = 'nm'

Expand Down

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