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