Patch install

pyproject.toml

@@ -64,19 +64,28 @@ dependencies = [
 [project.optional-dependencies]
 docs = [
     "sphinx>=5.0",
-    "sphinx-rtd-theme>=1.0", 
+    "sphinx-rtd-theme>=1.0",
     "myst-parser>=0.18",
     "sphinx-autobuild>=2021.3.14",
     "linkify-it-py>=2.0"
 ]
 bo = [
     "torch",
-    "botorch", 
+    "botorch",
     "gpytorch"
 ]
 abc = [
     "pyabc"
 ]
+gui = [
+    "pyqt5",
+    "seaborn",
+]
+all =
+    "uq_physicell[bo]",
+    "uq_physicell[abc]",
+    "uq_physicell[gui]",
+]
 
 [project.scripts]
 uq_physicell = "uq_physicell.gui.main_window:main"

uq_physicell/database/ma_db.py

@@ -728,7 +728,7 @@ def check_simulations_db(PhysiCellModel: PhysiCell_Model, sampler: str, param_di
         for sample_id, params in dic_samples.items():
             # Use set items comparison to ignore order of keys
             if set(dic_samples_db[sample_id].items()) != set(params.items()):
-                raise ValueError(f"ParameterSpace mismatch for SampleID {sample_id}. Expected: {params}, Found: {dic_samples_db[sample_id]}.")
+                raise ValueError(f"ParameterSpace mismatch for SampleID {sample_id}. Expected: {sorted(params.items())}, Found: {sorted(dic_samples_db[sample_id].items())}.")
 
         # Check if QoIs match the expected values
         if qois_dic:
@@ -813,4 +813,4 @@ def get_database_type(db_file: str) -> bool:
     elif 'BO_Method' in columns:
         return "BO"
     else:
-        return None
+        return None

uq_physicell/gui/tab1_select_params.py

@@ -111,7 +111,7 @@ def create_tab1(main_window):
     main_window.combo_box.setEnabled(False)
     main_window.combo_hbox.addWidget(main_window.combo_box)
     main_window.combo_hbox.addStretch()
-    
+
     # Create a group box for parameter details
     main_window.param_details_groupbox = QGroupBox("Parameter Details")
     param_details_layout = QVBoxLayout()
@@ -151,12 +151,12 @@ def create_tab1(main_window):
         lambda: [
             main_window.set_param_button.setEnabled(main_window.new_value_input.text().strip() != ""),
             main_window.set_param_button.setStyleSheet(
-                "background-color: lightgreen; color: black;" if main_window.new_value_input.text().strip() 
+                "background-color: lightgreen; color: black;" if main_window.new_value_input.text().strip()
                 else "background-color: lightgreen; color: darkgray;"
             ),
             main_window.add_analysis_button.setEnabled(not main_window.set_param_button.isEnabled()),
             main_window.add_analysis_button.setStyleSheet(
-                "background-color: lightgreen; color: black;" if not main_window.new_value_input.text().strip() 
+                "background-color: lightgreen; color: black;" if not main_window.new_value_input.text().strip()
                 else "background-color: lightgreen; color: darkgray;"
             )
         ]
@@ -264,6 +264,10 @@ def create_combo_box(main_window, parent_node, label):
         # Append the 'index' attribute if it exists
         if "index" in child.attrib:
             display_name = f"{display_name}[{int(child.get('index')) + 1}]"
+        # Append the 'ID' attribute for Dirichlet_options boundary_value
+        elif display_name == "boundary_value":
+            display_name = f"{display_name}[@ID='" + child.get('ID') + "']"
+        # Generic
         combo_box.addItem(display_name)
     combo_box.currentIndexChanged.connect(lambda: main_window.handle_combo_selection(main_window, combo_box, parent_node))
 
@@ -295,6 +299,9 @@ def handle_combo_selection(main_window, combo_box, parent_node):
         display_name = child.get("name", child.tag)
         if "index" in child.attrib:
             display_name = f"{display_name}[{int(child.get('index')) + 1}]"
+        elif display_name == "boundary_value":
+            display_name = f"{display_name}[@ID='{child.get('ID')}']"
+
         if display_name == selected_display_name:
             # Clear combo boxes below the current one
             main_window.clear_combo_boxes(main_window, starting_index=main_window.combo_hbox.indexOf(combo_box) + 1)
@@ -313,7 +320,6 @@ def handle_combo_selection(main_window, combo_box, parent_node):
                 main_window.update_selected_param_label(main_window, path, value)
             break
 
-
 def update_selected_param_label(main_window, path, value):
     # Determine the displayed value
     new_value = ''
@@ -436,12 +442,12 @@ def create_rule_section(main_window):
         lambda: [
             set_rule_button.setEnabled(main_window.new_value_input_rule.text().strip() != ""),
             set_rule_button.setStyleSheet(
-                "background-color: lightgreen; color: black;" if main_window.new_value_input_rule.text().strip() 
+                "background-color: lightgreen; color: black;" if main_window.new_value_input_rule.text().strip()
                 else "background-color: lightgreen; color: darkgray;"
             ),
             add_rule_analysis_button.setEnabled(not set_rule_button.isEnabled()),
             add_rule_analysis_button.setStyleSheet(
-                "background-color: lightgreen; color: black;" if not main_window.new_value_input_rule.text().strip() 
+                "background-color: lightgreen; color: black;" if not main_window.new_value_input_rule.text().strip()
                 else "background-color: lightgreen; color: darkgray;"
             )
         ]
@@ -651,8 +657,11 @@ def get_parameter_path_xml(main_window, node):
         if "name" in node.attrib:
             node_name += f"[@name='{node.get('name')}']"
         # Append 'index' attribute if it exists
-        if "index" in node.attrib:
+        elif "index" in node.attrib:
             node_name += f"[{int(node.get('index')) + 1}]"
+        # Use ID attribute if Dirichlet_options boundary_value
+        elif "boundary_value" == node.tag :
+            node_name += f"[@ID='{node.get('ID')}']"
         path.insert(0, node_name)
         node = main_window.parent_map.get(node)  # Use the parent map to find the parent
     return ".//" + "/".join(path)
@@ -844,8 +853,8 @@ def save_ini_file(main_window):
                 config.read(file_path)
                 if struc_name in config.sections():
                     # Ask the user if they want to overwrite
-                    reply = QMessageBox.question(main_window, "Overwrite Confirmation", 
-                                                    f"Structure '{struc_name}' already exists. Do you want to overwrite it?", 
+                    reply = QMessageBox.question(main_window, "Overwrite Confirmation",
+                                                    f"Structure '{struc_name}' already exists. Do you want to overwrite it?",
                                                     QMessageBox.Yes | QMessageBox.No, QMessageBox.No)
                     if reply == QMessageBox.Yes:
                         # Remove the existing section

uq_physicell/model_analysis/utils.py

@@ -121,7 +121,7 @@ def mcds_list_to_qoi_df_long(recreated_qoi_funcs, all_sample_ids, chunk_size, db
                         and ReplicateID, with columns for each QoI - columns combined with time points.
     """
     # Process samples in chunks to avoid memory issues
-    ls_column = ['SampleID','ReplicateID', 'time'] + sorted(recreated_qoi_funcs.keys())
+    ls_column = ['SampleID','time','ReplicateID'] + sorted(recreated_qoi_funcs.keys())
     llo_data = []
     for i in range(0, len(all_sample_ids), chunk_size):
         chunk_sample_ids = all_sample_ids[i:i + chunk_size]
@@ -134,19 +134,20 @@ def mcds_list_to_qoi_df_long(recreated_qoi_funcs, all_sample_ids, chunk_size, db
                 mcds_ts_list = df_sample[df_sample['ReplicateID'] == ReplicateID]['Data'].values[0]
                 # print(f"SampleID: {SampleID}, ReplicateID: {ReplicateID} - mcds_ts_list: {mcds_ts_list}")
                 for mcds in mcds_ts_list:
-                    lo_data = [SampleID, ReplicateID, mcds.get_time()]
+                    lo_data = [SampleID, mcds.get_time(), ReplicateID]
                     try:
                         for qoi_name, qoi_func in sorted(recreated_qoi_funcs.items()):
                             # Store functions the qoi result
                             function_result = safe_call_qoi_function(qoi_func, mcds=mcds, list_mcds=mcds_ts_list)
                             lo_data.append(function_result)
                     except Exception as e:
-                        raise RuntimeError(f"Error calculating QoIs for SampleID: {SampleID}, ReplicateID: {ReplicateID} - QoI: {qoi_name}_{id_time}: {e}")
+                        raise RuntimeError(f"Error calculating QoIs for SampleID: {SampleID}, ReplicateID: {ReplicateID} - QoI: {qoi_name} {qoi_func}: {e}")
                     # Store the mcds results
                     llo_data.append(lo_data)
 
     # Gernate data frame
     df_qois = pd.DataFrame(llo_data, columns=ls_column)
+    df_qois = df_qois.sort_values(['SampleID','time','ReplicateID'], ignore_index=True)
     return df_qois
 
 def mcds_list_to_qoi_df_for_calib(recreated_qoi_funcs, all_sample_ids, chunk_size, db_file) -> pd.DataFrame:

uq_physicell/pc_model.py

@@ -512,6 +512,8 @@ def _set_xml_element_value(xml_root: ET.Element, key: str, val: Union[str, int,
     # Check and extract the attribute name using regex
     attribute = _attr_name_re.search(last_seg)
     elem = elems[0]
+    if last_seg.startswith('boundary_value[@ID'):
+        attribute = False
     if attribute:
         elem.set(attribute.group(1), str(val))
     else:
@@ -780,4 +782,4 @@ def compile_physicell(pc_path, model_path, executable_path=None, force_compile=F
 
     finally:
         # Restore original working directory
-        os.chdir(original_cwd)
+        os.chdir(original_cwd)