Merge pull request #90 from PhysiCell-Tools/development

Development

bin/config_tab.py

@@ -688,7 +688,7 @@ def fill_xml(self):
         self.xml_root.find(".//dt_mechanics").text = self.mechanics_dt.text()
         self.xml_root.find(".//dt_phenotype").text = self.phenotype_dt.text()
         self.xml_root.find(".//omp_num_threads").text = self.num_threads.text()
-        self.xml_root.find(".//folder").text = self.folder.text()
+        self.xml_root.find(".//save//folder").text = self.folder.text()
         # print(f'------- config_tab.py: fill_xml(): setting folder = {self.folder.text()}')
 
         if self.save_svg.isChecked():

bin/rules_tab.py

@@ -150,6 +150,7 @@ def __init__(self, nanohub_flag, microenv_tab, celldef_tab):
 
         self.nanohub_flag = nanohub_flag
         self.homedir = '.'  # reset in studio.py
+        self.absolute_data_dir = None   # updated in studio.py
 
         self.microenv_tab = microenv_tab
         self.celldef_tab = celldef_tab
@@ -406,13 +407,13 @@ def __init__(self, nanohub_flag, microenv_tab, celldef_tab):
 
         #---
         label = QLabel("")
-        lwidth = 120
+        lwidth = 60
         label.setFixedWidth(lwidth)
         hlayout.addWidget(label) 
 
         #---
-        label = QLabel("Max")
-        label.setFixedWidth(30)
+        label = QLabel("Max response")
+        label.setFixedWidth(90)
         # label.setAlignment(QtCore.Qt.AlignRight)
         label.setAlignment(QtCore.Qt.AlignCenter)
         hlayout.addWidget(label) 

data/cell_rules.csv

@@ -0,0 +1,24 @@
+malignant epithelial cell,oxygen,decreases,necrosis,0,3.75,8,0
+malignant epithelial cell,oxygen,increases,cycle entry,0.003333,21.5,4,0
+malignant epithelial cell,pressure,decreases,cycle entry,0,1,4,0
+malignant epithelial cell,apoptotic,increases,apoptotic debris secretion,0.017,0.1,10,1
+malignant epithelial cell,necrotic,increases,necrotic debris secretion,0.017,0.1,10,1
+malignant epithelial cell,oxygen,decreases,migration speed,0,5,4,0
+malignant epithelial cell,damage,increases,apoptosis,0.1,5,8,0
+M0 macrophage,necrotic debris,increases,transform to M1 macrophage,0.05,0.005,4,0
+M0 macrophage,apoptotic debris,decreases,migration speed,0.1,0.005,4,0
+M0 macrophage,necrotic debris,decreases,migration speed,0.1,0.005,4,0
+M0 macrophage,volume,decreases,phagocytose dead cell,0,6000,4,0
+M1 macrophage,oxygen,decreases,transform to M2 macrophage,0.0001,5,8,0
+M1 macrophage,apoptotic debris,decreases,migration speed,0.1,0.005,4,0
+M1 macrophage,necrotic debris,decreases,migration speed,0.1,0.005,4,0
+M1 macrophage,volume,decreases,phagocytose dead cell,0.0,6000,4,0
+M2 macrophage,apoptotic debris,decreases,migration speed,0.1,0.005,4,0
+M2 macrophage,necrotic debris,decreases,migration speed,0.1,0.005,4,0
+M2 macrophage,volume,decreases,phagocytose dead cell,0.0,6000,4,0
+effector T cell,pro-inflammatory factor,increases,attack malignant epithelial cell,0.01,1,4,0
+effector T cell,contact with malignant epithelial cell,decreases,migration speed,0.01,0.1,10,0
+effector T cell,pro-inflammatory factor,increases,migration speed,1,0.01,4,0
+effector T cell,anti-inflammatory factor,increases,transform to exhausted T cell,0.001,0.5,4,0
+exhausted T cell,anti-inflammatory factor,decreases,migration speed,0.001,0.5,4,0
+exhausted T cell,contact with malignant epithelial cell,decreases,migration speed,0.01,0.1,10,0