-
Notifications
You must be signed in to change notification settings - Fork 0
/
main.py
251 lines (201 loc) · 10.7 KB
/
main.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
# -*- coding: utf-8 -*-
# Copyrights (c), 2020, Rinat Mukhometzianov
import pandas as pd
import matplotlib.pyplot as plt
import PySimpleGUI as sg
from os.path import exists
from os.path import join
class DataProcessing:
def __init__(self):
# CSV tables from ADNI website
self.merge_file = join('CSVs', 'ADNIMERGE.csv')
# Fields to read from a ADNIMERGE file
self.fields = ['RID', 'PTID', 'AGE', 'COLPROT', 'EXAMDATE', 'Month', 'DX', 'DX_bl', 'VISCODE']
self.filtered_groups = None
def is_merge_exists(self):
# Check if ADNIMERGE.csv file is available
return exists(self.merge_file)
@staticmethod
def change_dementia_naming(diags):
new_diags = []
for i, elem in enumerate(diags):
new_diags.append("Dementia" if elem == "AD" else diags[i])
return new_diags
def select_and_generate(self, stages, diags, age, age_range, stable_only):
adni_full = pd.read_csv(self.merge_file, skipinitialspace=True, usecols=self.fields)
alt_diags = self.change_dementia_naming(diags)
if len(diags) == 1:
if diags[0] == 'EMCI' or diags[0] == 'LMCI':
# for classification group selection
self.filtered_groups = adni_full[adni_full.COLPROT.isin(stages) & adni_full.DX_bl.isin(diags)]
else:
self.filtered_groups = adni_full[adni_full.COLPROT.isin(stages) & (adni_full.DX.isin(alt_diags) |
adni_full.DX_bl.isin(diags))]
if age != 0.0:
self.filtered_groups = self.filtered_groups[self.filtered_groups.AGE.between(age - age_range,
age + age_range)]
self.filtered_groups = self.filtered_groups.sort_values(by=['Month'])
if stable_only:
self.filtered_groups = self.filtered_groups.dropna(subset=['DX'])
groups = self.filtered_groups.groupby('RID', sort=False)
self.filtered_groups = groups.filter(lambda x: x.DX.eq(alt_diags[0]).all())
else:
phase = adni_full[adni_full.COLPROT.isin(stages) & adni_full.DX.isin(alt_diags)]
if age != 0.0:
phase = phase[phase.AGE.between(age - age_range, age + age_range)]
phase = phase.sort_values(by=['Month'])
groups = phase.groupby('RID', sort=False)
# Filter subjects that are converged from alt_diags[0] to alt_diags[1]
self.filtered_groups = groups.filter(lambda x:
x.DX.eq(alt_diags[0]).values[0] &
x.DX.eq(alt_diags[1]).values[-1])
u_ptids = self.filtered_groups.PTID.unique()
return self.filtered_groups, u_ptids
def find_rid_ranges(self):
"""
:return first and the last date of the subject
"""
ptid_groups = self.filtered_groups.groupby('PTID', sort=False)
frame = pd.DataFrame({'\u3000\u3000\u3000First': ptid_groups.first().EXAMDATE,
'\u3000\u3000Last': ptid_groups.last().EXAMDATE})
return frame.to_string()
class GUI:
def __init__(self):
sg.theme('default1')
# Visual layout
self.main_layout = [
[
sg.Frame(layout=[
[sg.Checkbox('ADNI-1', default=True, size=(7, 1), font=("Open Sans", 11)),
sg.Checkbox('ADNI-GO', size=(7, 1), font=("Open Sans", 11)),
sg.Checkbox('ADNI-2', size=(7, 1), font=("Open Sans", 11)),
sg.Checkbox('ADNI-3', size=(7, 1), font=("Open Sans", 11))]
], title='Select ADNI phase(s)', relief=sg.RELIEF_SUNKEN, font=("Open Sans", 14))
],
[
sg.Frame(layout=[
[sg.Radio('CN->MCI', "g", default=True, size=(8, 1), font=("Open Sans", 11)),
sg.Radio('CN->AD', "g", size=(8, 1), font=("Open Sans", 11)),
sg.Radio('MCI->AD', "g", size=(8, 1), font=("Open Sans", 11))]
], title='Converged subjects', relief=sg.RELIEF_SUNKEN, font=("Open Sans", 14))
],
[
sg.Frame(layout=[
[sg.Radio('CN', "g", size=(8, 1), font=("Open Sans", 11)),
sg.Radio('MCI', "g", size=(8, 1), font=("Open Sans", 11)),
sg.Radio('AD', "g", size=(8, 1), font=("Open Sans", 11))],
[sg.Radio('EMCI', "g", size=(8, 1), font=("Open Sans", 11)),
sg.Radio('LMCI', "g", size=(8, 1), font=("Open Sans", 11)),
sg.Checkbox('stable only?', font=("Open Sans", 11), default=True, key='-is-stable-',
tooltip='Include subjects that have been converged to other groups?')]
], title='Classification groups', relief=sg.RELIEF_SUNKEN, font=("Open Sans", 14))
],
[sg.Text('Age', font=("Open Sans", 11)),
sg.InputText(size=(5, 1), default_text='60.0', font=("Open Sans", 10), key='-age-'),
sg.Text(u'\xb1', font=("Default 12", 12)), # plus minus symbol
sg.InputText(size=(5, 1), default_text='5.0', font=("Open Sans", 10), key='-age-range-'),
sg.Checkbox('Save to file', font=("Open Sans", 11), key='-is-save-file-')],
[sg.Text('Subject IDs', font=("Open Sans", 16))],
[sg.Multiline(key='-res_rid-', size=(50, 7))],
[sg.Text('Subject IDs date ranges', font=("Open Sans", 16))],
[sg.Multiline(key='-res-rid-dates-', size=(50, 7))],
[sg.Button('Select', font=("Open Sans", 14)),
sg.Button('Distr', font=("Open Sans", 14))]
]
self.main_window = sg.Window('Select subjects', self.main_layout, grab_anywhere=False)
# Maps for many only
self.menu_map_stage = dict([(0, 'ADNI1'),
(1, 'ADNIGO'),
(2, 'ADNI2'),
(3, 'ADNI3')
])
self.menu_map_group = dict([(4, ['CN', 'MCI']),
(5, ['CN', 'AD']),
(6, ['MCI', 'AD']),
(7, ['CN']),
(8, ['MCI']),
(9, ['AD']),
(10, ['EMCI']),
(11, ['LMCI'])
])
self.values = None
self.event = None
self.dp = DataProcessing()
def age_check(self):
"""
Check if the user input age is indeed float point
:return: return 'clean' age and range for it
"""
age = 0.0
age_range = 0.0
if self.values['-age-'].replace('.', '', 1).isdigit() and \
self.values['-age-range-'].replace('.', '', 1).isdigit():
age = float(self.values['-age-'])
age_range = float(self.values['-age-range-'])
if age < 0.0 or age_range < 0.0:
sg.Popup('Age can\'t be negative. Will be ignored in the final output.')
age = 0.0
age_range = 0.0
else:
sg.Popup('Your input in the Age field is not a real value. Will be ignored in the final output.')
return age, age_range
def groups_stages(self):
stages = [self.menu_map_stage[i] for i in range(4) if self.values[i]]
groups = [self.menu_map_group[i] for i in range(4, 12) if self.values[i]][0]
return stages, groups
def select_button(self):
age, age_range = self.age_check()
age_file_name = str(age - age_range) + '-' + str(age + age_range) if age != 0.0 else ''
stages, groups = self.groups_stages()
_, res = self.dp.select_and_generate(stages, groups, age, age_range, self.values['-is-stable-'])
res_rid = ', '.join([str(i) for i in res])
if res_rid == '': # if no results with specified input params
no_results_text = 'No results for the specified input!'
self.main_window['-res_rid-'].update(no_results_text)
self.main_window['-res-rid-dates-'].update(no_results_text)
else:
self.main_window['-res_rid-'].update(res_rid)
# Update window with fist and last date of exam for each subject
res_rid_dates = self.dp.find_rid_ranges()
self.main_window['-res-rid-dates-'].update(res_rid_dates)
# Write to file if selected and there are results to write
if self.values['-is-save-file-']:
self.write_to_file(stages, groups, age_file_name, res_rid, res_rid_dates)
def show_distributions_button(self):
stages, groups = self.groups_stages()
# make strings for graph title
stages_string = ', '.join([str(i) for i in stages])
groups_string = '->'.join([str(i) for i in groups])
# get subset of subjects independent of their age
res, _ = self.dp.select_and_generate(stages, groups, 0, 0, self.values['-is-stable-'])
# Run graph
ax = res.hist(column='AGE', grid=False)
x = ax[0, 0]
x.spines['right'].set_visible(False)
x.spines['top'].set_visible(False)
x.spines['left'].set_visible(False)
x.set_title("Age distribution for "+groups_string+" in "+stages_string)
plt.show()
def run(self):
while True:
self.event, self.values = self.main_window.read()
if self.dp.is_merge_exists():
if self.event == 'Select':
self.select_button()
elif self.event == 'Distr':
self.show_distributions_button()
else:
sg.Popup('ADNIMERGE.csv not found!', 'Please, put it in the CSVs folder and restart the program.')
if self.event == sg.WINDOW_CLOSED or self.event == 'Exit':
break
self.main_window.close()
@staticmethod
def write_to_file(stages, groups, fn, res_rid, dates):
with open('_'.join(stages) + '_' + '_'.join(groups) + '_' + fn + '.txt', 'w', encoding='utf-8') as f:
f.write("Subject IDs:\n")
f.write(res_rid)
f.write("\n\n")
f.write("Subject IDs and date ranges:\n")
f.write(dates)
g = GUI()
g.run()