Merge pull request #246 from PhysiCell-Tools/development

bug fixes for boolean intracellular UI; radio buttons on Config tab

Author: rheiland

VERSION.txt

@@ -1 +1 @@
-2.38.0
+2.39.1

bin/cell_def_tab.py

@@ -66,6 +66,28 @@ def __init__(self, studio_flag):
 
         # self.tab = QWidget()
         # self.tabs.resize(200,5)
+
+        radiobutton_style = """
+            QRadioButton {
+                spacing: 10px; /* Space between indicator and text */
+                color: black; /* Text color */
+            }
+
+            QRadioButton::indicator {
+                width: 12px; /* Indicator size */
+                height: 12px;
+                border-radius: 6px; /* Rounded indicator */
+            }
+
+            QRadioButton::indicator:unchecked {
+                border: 1px solid gray; /* Border when unchecked */
+            }
+
+            QRadioButton::indicator:checked {
+                background-color: rgb(21,96,209); /* Filled color when checked */
+                border: 1px solid black;
+            }
+                """
 
         #-------------------------------------------
         label_width = 110
@@ -329,13 +351,12 @@ def __init__(self, studio_flag):
         self.random_seed_gp.idToggled.connect(self.random_seed_gp_cb)
         random_seed_gp_next_id = 0
 
-        self.random_seed_random_button = QRadioButton("system clock")
-        self.random_seed_random_button.setChecked(True)
+        self.random_seed_random_button = QRadioButton("system clock",styleSheet=radiobutton_style)
         self.random_seed_gp.addButton(self.random_seed_random_button, random_seed_gp_next_id)
         hbox.addWidget(self.random_seed_random_button)
         random_seed_gp_next_id += 1
 
-        self.random_seed_integer_button = QRadioButton("integer \u2192 ")
+        self.random_seed_integer_button = QRadioButton("integer \u2192 ",styleSheet=radiobutton_style)
         self.random_seed_gp.addButton(self.random_seed_integer_button, random_seed_gp_next_id)
         hbox.addWidget(self.random_seed_integer_button)
         random_seed_gp_next_id += 1
@@ -708,7 +729,8 @@ def fill_gui(self):
         if self.xml_root.find(".//random_seed") is not None:
             # this intentionally will read in the user_parameter random_seed if it exists. this will facilitate the user using this new placement (importantly, the default custom.cpp will still use the user_parameter to override the value placed here)
             text = self.xml_root.find(".//random_seed").text
-            if text in  ["system_clock","random",""]:
+            print("\n------------------ config_tab: random_seed = ",text)
+            if text in  ["system_clock","random","",None]:
                 self.random_seed_random_button.setChecked(True)
             else:
                 self.random_seed_integer_button.setChecked(True)

bin/config_tab.py

@@ -1403,6 +1403,9 @@ def populate_tree_cell_defs(cell_def_tab, skip_validate):
                                 cell_def_tab.param_d[cell_def_name]["intracellular"]["parameters"].append({"name": parameter.attrib["intracellular_name"], "value": parameter.text})                    
 
                     # print("cell def : " + cell_def_name + " : dt = " + cell_def_tab.param_d[cell_def_name]["intracellular"]["time_step"])
+                    # <initial_values>
+                    #     <initial_value intracellular_name="A">1</initial_value>
+                    #     <initial_value intracellular_name="C">0</initial_value>
                     cell_def_tab.param_d[cell_def_name]["intracellular"]["initial_values"] = []
                     uep_intracellular_iv = uep_intracellular.find("initial_values")
                     if uep_intracellular_iv is not None:
@@ -1469,13 +1472,28 @@ def populate_tree_cell_defs(cell_def_tab, skip_validate):
                     #     <map PC_phenotype="ctr_0_0" sbml_species="Transition_Rate"/>
                     cell_def_tab.param_d[cell_def_name]["intracellular"]["type"] = "roadrunner" 
 
-                    msg = f"WARNING: a roadrunner intracellular model was detected, but it is not currently possible to modify its parameters from the Studio."
-                    print(msg)
-                    msgBox = QMessageBox()
-                    # msgBox.setTextFormat(Qt.RichText)
-                    msgBox.setText(msg)
-                    msgBox.setStandardButtons(QMessageBox.Ok)
-                    returnValue = msgBox.exec()
+                    cell_def_tab.param_d[cell_def_name]["intracellular"]["sbml_filename"] = uep_intracellular.find("sbml_filename").text if uep_intracellular.find("sbml_filename") is not None else None
+                    cell_def_tab.param_d[cell_def_name]["intracellular"]["intracellular_dt"] = uep_intracellular.find("intracellular_dt").text if uep_intracellular.find("intracellular_dt") is not None else None
+
+                    cell_def_tab.param_d[cell_def_name]["intracellular"]["sbml_maps"] = []
+                    for mymap in uep_intracellular.findall('map'):
+                        # save triplets 
+                        if 'PC_substrate' in mymap.attrib.keys():
+                            cell_def_tab.param_d[cell_def_name]["intracellular"]["sbml_maps"].append(['PC_substrate',mymap.attrib['PC_substrate'], mymap.attrib['sbml_species'] ])
+                        elif 'PC_phenotype' in mymap.attrib.keys():
+                            cell_def_tab.param_d[cell_def_name]["intracellular"]["sbml_maps"].append(['PC_phenotype',mymap.attrib['PC_phenotype'], mymap.attrib['sbml_species'] ])
+                        elif 'PC_custom_data' in mymap.attrib.keys():
+                            cell_def_tab.param_d[cell_def_name]["intracellular"]["sbml_maps"].append(['PC_custom_data',mymap.attrib['PC_custom_data'], mymap.attrib['sbml_species'] ])
+
+                    print("\n--> ",cell_def_tab.param_d[cell_def_name]["intracellular"]["sbml_maps"])
+
+                    # msg = f"WARNING: a roadrunner intracellular model was detected, but it is not currently possible to modify its parameters from the Studio."
+                    # print(msg)
+                    # msgBox = QMessageBox()
+                    # # msgBox.setTextFormat(Qt.RichText)
+                    # msgBox.setText(msg)
+                    # msgBox.setStandardButtons(QMessageBox.Ok)
+                    # returnValue = msgBox.exec()
 
 
             logging.debug(f'------ done parsing intracellular:')

bin/populate_tree_cell_defs.py

@@ -2128,7 +2128,7 @@ def fill_gui(self):
             # self.rules_text.setPlainText("")
             self.rules_folder.setText("config")
             self.rules_file.setText("rules.csv")
-            self.rules_enabled.setChecked(True)
+            # self.rules_enabled.setChecked(True)   # Sep 2024: comment out; error w/ physiboss model with no rules block provided in xml 
 
             self.clear_rules()
         return