-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathREADME
More file actions
288 lines (279 loc) · 15.4 KB
/
Copy pathREADME
File metadata and controls
288 lines (279 loc) · 15.4 KB
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
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
Setup
=====
cat pdac.sql | sqlite3
Usage
=====
Rscript -e " rmarkdown::render( 'binary_analysis.RMD', output_file = './binary_exampleout.pdf', params = list( csvPath='dicom/radiomicsgrowout.csv', outCsvName = 'exampledata_binary_withpredictions.csv',target='target', positive_class='High', regexp='(original_firstorder|original_glcm|original_glrlm|original_glszm)', fixed_inputs=NULL,leaveOneOut=TRUE, nfold=NULL, foldID=NULL, rescale=FALSE, removeCorrelated=TRUE, plot=TRUE, l1lasso=TRUE, univariate=TRUE, unipValThresh=0.05,cutoff=.7 ) )"
TF Usage
=====
python lrmodel.py --databaseid=phmda --initialize
python lrmodel.py --databaseid=phmda --setuptestset
python lrmodel.py --databaseid=phmda --builddb
make -f phmda256kfold010.makefile models
tensorboard --logdir=./phmdalog/ --port=6010
make -f lrstatistics.makefile labels
make -j 8 -B -k -i -f lrstatistics.makefile lstat
cat qastats/*/lstat.csv > qastats/lstat.csv
cat lrstatistics.sql | sqlite3
R ; source('lrstats.R')
TF Usage
=====
python lrmodel.py --databaseid=lrmda --initialize
python lrmodel.py --databaseid=lrmda --setuptestset
python lrmodel.py --databaseid=lrmda --setuptestset --trainingloss=dscwgthi
python lrmodel.py --databaseid=lrmda --builddb
make -f lrmdadscimg256kfold010.makefile models
make -f lrmdadscwgthi256kfold010.makefile models
tensorboard --logdir=./lrmdalog/ --port=6010
make MODELID=lrmdadscimg -f lrstatistics.makefile labels
make MODELID=lrmdadscwgthi -f lrstatistics.makefile labels
make MODELID=lrmdadscimg -j 8 -B -k -i -f lrstatistics.makefile lstat
make MODELID=lrmdadscwgthi -j 8 -B -k -i -f lrstatistics.makefile lstat
cat qastats/lrmdapocketdscimg/*/lstat.csv > qastats/lrmdapocketdscimg/lstat.csv
cat qastats/lrmdapocketdscwgthi/*/lstat.csv > qastats/lrmdapocketdscwgthi/lstat.csv
cat lrstatistics.sql | sqlite3
R ; source('lrstats.R')
Rscript lrstats.R
Dependencies
======
$ conda list
# packages in environment at /opt/apps/miniconda/tf2:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 4.5 1_gnu
_tflow_select 2.1.0 gpu
absl-py 0.15.0 pyhd3eb1b0_0
aiohttp 3.8.1 py38h7f8727e_1
aiosignal 1.2.0 pyhd3eb1b0_0
argon2-cffi 21.3.0 pyhd3eb1b0_0
argon2-cffi-bindings 21.2.0 py38h7f8727e_0
astor 0.8.1 py38h06a4308_0
asttokens 2.0.5 pyhd3eb1b0_0
astunparse 1.6.3 py_0
async-timeout 4.0.1 pyhd3eb1b0_0
attrs 21.4.0 pyhd3eb1b0_0
backcall 0.2.0 pyhd3eb1b0_0
beautifulsoup4 4.11.1 py38h06a4308_0
blas 1.0 mkl
bleach 4.1.0 pyhd3eb1b0_0
blinker 1.4 py38h06a4308_0
bottleneck 1.3.4 py38hce1f21e_0
brotli 1.0.9 he6710b0_2
brotlipy 0.7.0 py38h27cfd23_1003
c-ares 1.18.1 h7f8727e_0
ca-certificates 2022.4.26 h06a4308_0
cachetools 4.2.2 pyhd3eb1b0_0
certifi 2021.10.8 py38h06a4308_2
cffi 1.14.3 py38h261ae71_2
chardet 3.0.4 py38h06a4308_1003
charset-normalizer 2.0.4 pyhd3eb1b0_0
click 8.0.4 py38h06a4308_0
cloudpickle 2.0.0 pyhd3eb1b0_0
conda 4.12.0 py38h06a4308_0
conda-package-handling 1.7.2 py38h03888b9_0
cryptography 3.2.1 py38h3c74f83_1
cudatoolkit 10.1.243 h6bb024c_0
cudnn 7.6.5 cuda10.1_0
cupti 10.1.168 0
cycler 0.11.0 pyhd3eb1b0_0
cytoolz 0.11.0 py38h7b6447c_0
dask-core 2022.2.1 pyhd3eb1b0_0
dataclasses 0.8 pyh6d0b6a4_7
dbus 1.13.18 hb2f20db_0
debugpy 1.5.1 py38h295c915_0
decorator 5.1.1 pyhd3eb1b0_0
defusedxml 0.7.1 pyhd3eb1b0_0
entrypoints 0.4 py38h06a4308_0
executing 0.8.3 pyhd3eb1b0_0
expat 2.4.4 h295c915_0
fontconfig 2.13.1 h6c09931_0
fonttools 4.25.0 pyhd3eb1b0_0
freetype 2.11.0 h70c0345_0
frozenlist 1.2.0 py38h7f8727e_0
fsspec 2022.2.0 pyhd3eb1b0_0
gast 0.4.0 pyhd3eb1b0_0
giflib 5.2.1 h7b6447c_0
glib 2.69.1 h4ff587b_1
google-auth 1.28.0 pyhd3eb1b0_0
google-auth-oauthlib 0.4.4 pyhd3eb1b0_0
google-pasta 0.2.0 pyhd3eb1b0_0
grpcio 1.42.0 py38hce63b2e_0
gst-plugins-base 1.14.0 h8213a91_2
gstreamer 1.14.0 h28cd5cc_2
h5py 2.10.0 py38hd6299e0_1
hdf5 1.10.6 hb1b8bf9_0
icu 58.2 he6710b0_3
idna 2.10 py_0
imageio 2.9.0 pyhd3eb1b0_0
importlib-metadata 4.11.3 py38h06a4308_0
importlib_resources 5.2.0 pyhd3eb1b0_1
intel-openmp 2021.4.0 h06a4308_3561
ipykernel 6.9.1 py38h06a4308_0
ipython 8.3.0 py38h06a4308_0
ipython_genutils 0.2.0 pyhd3eb1b0_1
ipywidgets 7.6.5 pyhd3eb1b0_1
jedi 0.18.1 py38h06a4308_1
jinja2 3.0.3 pyhd3eb1b0_0
joblib 1.1.0 pyhd3eb1b0_0
jpeg 9e h7f8727e_0
jsonschema 4.4.0 py38h06a4308_0
jupyter 1.0.0 py38_7
jupyter_client 7.2.2 py38h06a4308_0
jupyter_console 6.4.3 pyhd3eb1b0_0
jupyter_core 4.10.0 py38h06a4308_0
jupyterlab_pygments 0.1.2 py_0
jupyterlab_widgets 1.0.0 pyhd3eb1b0_1
keras 2.8.0 pypi_0 pypi
keras-preprocessing 1.1.2 pyhd3eb1b0_0
kiwisolver 1.3.2 py38h295c915_0
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.33.1 h53a641e_7
libedit 3.1.20191231 h14c3975_1
libffi 3.3 he6710b0_2
libgcc-ng 9.3.0 h5101ec6_17
libgfortran-ng 7.5.0 ha8ba4b0_17
libgfortran4 7.5.0 ha8ba4b0_17
libgomp 9.3.0 h5101ec6_17
libpng 1.6.37 hbc83047_0
libprotobuf 3.19.1 h4ff587b_0
libsodium 1.0.18 h7b6447c_0
libstdcxx-ng 9.1.0 hdf63c60_0
libtiff 4.2.0 h85742a9_0
libuuid 1.0.3 h7f8727e_2
libwebp 1.2.2 h55f646e_0
libwebp-base 1.2.2 h7f8727e_0
libxcb 1.14 h7b6447c_0
libxml2 2.9.12 h03d6c58_0
locket 0.2.1 py38h06a4308_2
lz4-c 1.9.3 h295c915_1
markdown 3.3.4 py38h06a4308_0
markupsafe 2.0.1 py38h27cfd23_0
matplotlib 3.5.1 py38h06a4308_1
matplotlib-base 3.5.1 py38ha18d171_1
matplotlib-inline 0.1.2 pyhd3eb1b0_2
mistune 0.8.4 py38h7b6447c_1000
mkl 2021.4.0 h06a4308_640
mkl-service 2.4.0 py38h7f8727e_0
mkl_fft 1.3.1 py38hd3c417c_0
mkl_random 1.2.2 py38h51133e4_0
multidict 5.2.0 py38h7f8727e_2
munkres 1.1.4 py_0
nbclient 0.5.13 py38h06a4308_0
nbconvert 6.4.4 py38h06a4308_0
nbformat 5.3.0 py38h06a4308_0
ncurses 6.2 he6710b0_1
nest-asyncio 1.5.5 py38h06a4308_0
networkx 2.7.1 pyhd3eb1b0_0
nibabel 3.2.2 pypi_0 pypi
notebook 6.4.11 py38h06a4308_0
numexpr 2.8.1 py38h6abb31d_0
numpy 1.21.5 py38he7a7128_2
numpy-base 1.21.5 py38hf524024_2
oauthlib 3.1.0 py_0
openssl 1.1.1n h7f8727e_0
opt_einsum 3.3.0 pyhd3eb1b0_1
packaging 21.3 pyhd3eb1b0_0
pandas 1.4.2 py38h295c915_0
pandocfilters 1.5.0 pyhd3eb1b0_0
parso 0.8.3 pyhd3eb1b0_0
partd 1.2.0 pyhd3eb1b0_1
pcre 8.45 h295c915_0
pexpect 4.8.0 pyhd3eb1b0_3
pickleshare 0.7.5 pyhd3eb1b0_1003
pillow 9.0.1 py38h22f2fdc_0
pip 20.2.4 py38h06a4308_0
prometheus_client 0.13.1 pyhd3eb1b0_0
prompt-toolkit 3.0.20 pyhd3eb1b0_0
prompt_toolkit 3.0.20 hd3eb1b0_0
protobuf 3.19.1 py38h295c915_0
ptyprocess 0.7.0 pyhd3eb1b0_2
pure_eval 0.2.2 pyhd3eb1b0_0
pyasn1 0.4.8 pyhd3eb1b0_0
pyasn1-modules 0.2.8 py_0
pycosat 0.6.3 py38h7b6447c_1
pycparser 2.20 py_2
pydicom 2.3.0 pypi_0 pypi
pygments 2.11.2 pyhd3eb1b0_0
pyjwt 1.7.1 py38_0
pyopenssl 19.1.0 pyhd3eb1b0_1
pyparsing 3.0.4 pyhd3eb1b0_0
pyqt 5.9.2 py38h05f1152_4
pyrsistent 0.18.0 py38heee7806_0
pysocks 1.7.1 py38h06a4308_0
python 3.8.8 hdb3f193_4
python-dateutil 2.8.2 pyhd3eb1b0_0
python-fastjsonschema 2.15.1 pyhd3eb1b0_0
python-flatbuffers 2.0 pyhd3eb1b0_0
pytz 2021.3 pyhd3eb1b0_0
pywavelets 1.3.0 py38h7f8727e_0
pyyaml 6.0 py38h7f8727e_1
pyzmq 22.3.0 py38h295c915_2
qt 5.9.7 h5867ecd_1
qtconsole 5.3.0 pyhd3eb1b0_0
qtpy 2.0.1 pyhd3eb1b0_0
readline 8.0 h7b6447c_0
requests 2.24.0 py_0
requests-oauthlib 1.3.0 py_0
rsa 4.7.2 pyhd3eb1b0_1
ruamel_yaml 0.15.87 py38h7b6447c_1
scikit-image 0.19.2 py38h51133e4_0
scikit-learn 1.0.2 py38h51133e4_1
scipy 1.7.3 py38hc147768_0
send2trash 1.8.0 pyhd3eb1b0_1
setuptools 50.3.1 py38h06a4308_1
simpleitk 2.1.1.2 pypi_0 pypi
sip 4.19.13 py38h295c915_0
six 1.15.0 py38h06a4308_0
soupsieve 2.3.1 pyhd3eb1b0_0
sqlite 3.33.0 h62c20be_0
stack_data 0.2.0 pyhd3eb1b0_0
tensorboard 2.4.0 pyhc547734_0
tensorboard-plugin-wit 1.6.0 py_0
tensorflow 2.4.1 gpu_py38h8a7d6ce_0
tensorflow-base 2.4.1 gpu_py38h29c2da4_0
tensorflow-estimator 2.6.0 pyh7b7c402_0
tensorflow-gpu 2.4.1 h30adc30_0
termcolor 1.1.0 py38h06a4308_1
terminado 0.13.1 py38h06a4308_0
testpath 0.5.0 pyhd3eb1b0_0
threadpoolctl 2.2.0 pyh0d69192_0
tifffile 2020.10.1 py38hdd07704_2
tk 8.6.10 hbc83047_0
toolz 0.11.2 pyhd3eb1b0_0
tornado 6.1 py38h27cfd23_0
tqdm 4.51.0 pyhd3eb1b0_0
traitlets 5.1.1 pyhd3eb1b0_0
typing-extensions 4.1.1 hd3eb1b0_0
typing_extensions 4.1.1 pyh06a4308_0
urllib3 1.25.11 py_0
wcwidth 0.2.5 pyhd3eb1b0_0
webencodings 0.5.1 py38_1
werkzeug 2.0.3 pyhd3eb1b0_0
wheel 0.35.1 pyhd3eb1b0_0
widgetsnbextension 3.5.2 py38h06a4308_0
wrapt 1.13.3 py38h7f8727e_2
xz 5.2.5 h7b6447c_0
yaml 0.2.5 h7b6447c_0
yarl 1.6.3 py38h27cfd23_0
zeromq 4.3.4 h2531618_0
zipp 3.7.0 pyhd3eb1b0_0
zlib 1.2.11 h7b6447c_3
zstd 1.4.9 haebb681_0
TF Usage
=====
cat pdacgemcitabine.sql | sqlite3
make -f d2.makefile -j 12 -B roi
make -f d2.makefile -j 12 -B lesionmask
python /rsrch1/ip/dtfuentes/github/pocketnet/pdacpreprocess.py
python /rsrch1/ip/dtfuentes/github/pocketnet/classification.py
Rscript d2stats.R
tensorboard --logdir log
make -f d2.makefile dicom/radiomicsout.csv
Rscript longwide.R
GROW
=====
cat pdacgrow.sql | sqlite3
make -f grow.makefile raw
make -f grow.makefile truth
make -f grow.makefile dicom/radiomicsgrowout.csv