confM1.py

### Copyright (C) 2020-2023  Alessio Gianelle, INFN Padova
###
### This program is free software: you can redistribute it and/or modify
### it under the terms of the GNU General Public License as published by
### the Free Software Foundation, either version 3 of the License, or
### later version.
###
### This program is distributed in the hope that it will be useful,
### but WITHOUT ANY WARRANTY; without even the implied warranty of
### MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
### GNU General Public License for more details.
###
### You should found a copy of the GNU General Public License
### at this path: https://www.gnu.org/licenses/ .

datapath = "/home/gianelle/ML/marta/mitoMePo/dati/hdf"
testpath = "Result"
evalpath = "Eval"

datadir = 'M1-M4'
testpath += datadir
evalpath += datadir

namePopA = ['A375', 'HELA', 'HEK', 'PC9']
namePopB = ['M1', 'M2', 'M3', 'M4']

features = [u'REAL LIVING CELLS - Intensity Nuclei Mean',
       u'REAL LIVING CELLS - Intensity Nuclei StdDev',
       u'REAL LIVING CELLS - Intensity Nuclei Median',
       u'REAL LIVING CELLS - Intensity Nuclei Maximum',
       u'REAL LIVING CELLS - Intensity Nuclei Minimum',
       u'REAL LIVING CELLS - Intensity Nuclei Sum',
       u'REAL LIVING CELLS - Intensity Nuclei CV [%]',
       u'REAL LIVING CELLS - Intensity Nuclei Quantile 50%',
       u'REAL LIVING CELLS - Intensity Nuclei Contrast',
       u'REAL LIVING CELLS - Intensity Nucleus Resized Mean',
       u'REAL LIVING CELLS - Delta HOECHST',
       u'REAL LIVING CELLS - Nucleus Area [µm²]',
       u'REAL LIVING CELLS - Nucleus Roundness',
       u'REAL LIVING CELLS - Nucleus Width [µm]',
       u'REAL LIVING CELLS - Nucleus Length [µm]',
       u'REAL LIVING CELLS - Nucleus Ratio Width to Length',
       u'REAL LIVING CELLS - Nucleus Symmetry 02',
       u'REAL LIVING CELLS - Nucleus Symmetry 03',
       u'REAL LIVING CELLS - Nucleus Symmetry 04',
       u'REAL LIVING CELLS - Nucleus Symmetry 05',
       u'REAL LIVING CELLS - Nucleus Symmetry 12',
       u'REAL LIVING CELLS - Nucleus Symmetry 13',
       u'REAL LIVING CELLS - Nucleus Symmetry 14',
       u'REAL LIVING CELLS - Nucleus Symmetry 15',
       u'REAL LIVING CELLS - Nucleus Threshold Compactness 30%',
       u'REAL LIVING CELLS - Nucleus Threshold Compactness 40%',
       u'REAL LIVING CELLS - Nucleus Threshold Compactness 50%',
       u'REAL LIVING CELLS - Nucleus Threshold Compactness 60%',
       u'REAL LIVING CELLS - Nucleus Axial Small Length',
       u'REAL LIVING CELLS - Nucleus Axial Length Ratio',
       u'REAL LIVING CELLS - Nucleus Radial Mean',
       u'REAL LIVING CELLS - Nucleus Radial Relative Deviation',
       u'REAL LIVING CELLS - Nucleus Profile 4/5',
       u'REAL LIVING CELLS - Nucleus Profile 5/5',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Spot 0 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Hole 0 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Edge 0 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Ridge 0 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Valley 0 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Saddle 0 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Bright 0 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Dark 0 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 Haralick Correlation 1 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 Haralick Contrast 1 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 Haralick Sum Variance 1 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 Haralick Homogeneity 1 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 Gabor Min 2 px w2',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 Gabor Max 2 px w2']

reducedFeatures = [u'REAL LIVING CELLS - Intensity Nuclei Mean',
       u'REAL LIVING CELLS - Intensity Nuclei StdDev',
       u'REAL LIVING CELLS - Intensity Nuclei CV [%]',
       u'REAL LIVING CELLS - Nucleus Area [µm²]',
       u'REAL LIVING CELLS - Nucleus Roundness',
       u'REAL LIVING CELLS - Nucleus Width [µm]',
       u'REAL LIVING CELLS - Nucleus Length [µm]',
       u'REAL LIVING CELLS - Nucleus Ratio Width to Length',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Spot 0 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Hole 0 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Edge 0 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Ridge 0 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Valley 0 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Saddle 0 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Bright 0 px',
       u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Dark 0 px']

importanceFeatures = [u'REAL LIVING CELLS - Nucleus HOECHST 33342 Gabor Max 2 px w2',
u'REAL LIVING CELLS - Nucleus HOECHST 33342 Gabor Min 2 px w2',
u'REAL LIVING CELLS - Nucleus HOECHST 33342 Haralick Homogeneity 1 px',
u'REAL LIVING CELLS - Intensity Nuclei Contrast',
u'REAL LIVING CELLS - Intensity Nuclei Maximum',
u'REAL LIVING CELLS - Intensity Nuclei Minimum',
u'REAL LIVING CELLS - Intensity Nuclei StdDev',
u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Spot 0 px',
u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Hole 0 px',
u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Edge 0 px',
u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Ridge 0 px',
u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Valley 0 px',
u'REAL LIVING CELLS - Nucleus HOECHST 33342 SER Saddle 0 px']



