step3_classifyCells.groovy

/* Automated PD-L1 scoring of TPS, CPS, and ICS in whole slide images in a MATLAB/QuPath workflow
   Copyright (C) 2020-2021 Behrus Puladi
   https://orcid.org/0000-0001-5909-6105
   
   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 2
   of the License, or (at your option) any 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 have received a copy of the GNU General Public License
   along with this program; if not, write to the Free Software
   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA. */

// Load pre-trained model to classify the cells
def classifier = loadObjectClassifier("HNSCC_MLP_LYM_TUM_STR")

// Select all cells and the current image
def cells = getDetectionObjects().findAll {it.isCell()}
def imageData = getCurrentImageData()

// Classify cells
classifier.classifyObjects(imageData, cells, true)

// Apply the changes
fireHierarchyUpdate()