Bugfixes in interface

bin/substrates.py

@@ -983,7 +983,6 @@ class SubstrateTab(object):
                     
                 else:
                     if self.color_physiboss and self.color_physiboss_node is not None and self.color_physiboss_node[0] != '<':
-                        
                         if int(child.attrib['id'][4:]) in states_dict.keys():
                             if self.color_physiboss_node in states_dict[int(child.attrib['id'][4:])]:
                                 rgb = [0, 0.5, 0]

data/PhysiCell_settings.xml

@@ -113,7 +113,7 @@
 		</full_data>
 		
 		<SVG>
-			<interval units="min">15</interval>
+			<interval units="min">5</interval>
 			<enable>true</enable>
 		</SVG>
 		

data/create_cell_types_flat.py

+"""
+====================================================================================================
+  Parse a PhysiCell configuration file (XML) and generate a Jupyter (Python) module for 'Cell Types' GUI tab.
+  
+====================================================================================================
+ 
+  Inputs - takes none, 1, 2, 3, or 4 arguments
+  ------
+    config filename (str, optional): the PhysiCell configuration file (.xml) (Default = config.xml)
+    GUI module (str, optional):      the primary GUI for the Jupyter notebook 
+    colorname1, colorname2 (str, optional): the colors to use for the alternating rows of widgets 
+                                            (Defaults: lightgreen, tan)
+  Examples (with 0,1,2,3,4 args):
+  --------
+    python create_cell_types.py
+    python create_cell_types.py cells.xml
+  
+  Outputs
+  -------
+    cell_types.py: Python module used to create/edit cell parameters (--> "Cell Types" GUI tab)
+ 
+Authors:
+Randy Heiland (heiland@iu.edu)
+Dr. Paul Macklin (macklinp@iu.edu)
+
+--- Versions ---
+1.0 - initial version
+4.0 - (Oct 2020) for 'Cell Types' tab format, switched from using cell_definition inheritance style to "flat" (verbose) style
+
+"""
+
+import sys
+import os
+import math
+import xml.etree.ElementTree as ET
+
+# Defaults
+config_file = "config.xml"
+colorname1 = 'lightgreen'
+colorname2 = 'tan'
+color_idx = 0
+
+num_args = len(sys.argv)
+print("num_args=",num_args)
+if (num_args < 2):
+    print()
+    print("*** NOTE:  using config.xml  ***")
+    print()
+else:
+    config_file = sys.argv[1]
+    if not os.path.isfile(config_file):
+        print(config_file, "does not exist")
+        print("Usage: python " + sys.argv[0] + " <config-file.xml> [<gui-file.py>] [<colorname1> <colorname2>]")
+        sys.exit(1)
+
+if (num_args == 3):
+    gui_file = sys.argv[2]
+elif (num_args == 4):
+    colorname1 = sys.argv[2]
+    colorname2 = sys.argv[3]
+elif (num_args == 5):
+    gui_file = sys.argv[2]
+    colorname1 = sys.argv[3]
+    colorname2 = sys.argv[4]
+elif (num_args > 5):
+    print("Usage: python " + sys.argv[0] + " <config-file.xml> [<gui-file.py>] [<colorname1> <colorname2>]")
+    sys.exit(1)
+
+print()
+print("config_file = ",config_file)
+print("colorname1 = ",colorname1)
+print("colorname2 = ",colorname2)
+colorname = [colorname1,colorname2]
+print()
+
+if (num_args == 3):
+    with open(gui_file) as f:   # e.g., "mygui.py"
+    #  newText = f.read().replace('myconfig.xml', config_file) # todo: don't assume this string; find line
+        file_str = f.read()
+        idx = file_str.find('main_xml_filename')  # verify > -1
+        file_pre = file_str[:idx] 
+        idx2 = file_str[idx:].find('\n')
+        file_post = file_str[idx+idx2:] 
+
+    with open(gui_file, "w") as f:
+        f.write(file_pre)
+        f.write("main_xml_filename = '" + config_file + "'")
+        f.write(file_post)
+
+#---------------------------------------------------------------------------------------------------
+cells_tab_header = """ 
+# This file is auto-generated from a Python script that parses a PhysiCell configuration (.xml) file.
+#
+# Edit at your own risk.
+#
+import os
+from ipywidgets import Label,Text,Checkbox,Button,HBox,VBox,FloatText,IntText,BoundedIntText,BoundedFloatText,Layout,Box,Dropdown
+    
+class CellTypesTab(object):
+
+    def __init__(self):
+        
+        micron_units = Label('micron')   # use "option m" (Mac, for micro symbol)
+
+        constWidth = '180px'
+        tab_height = '500px'
+        stepsize = 10
+
+        #style = {'description_width': '250px'}
+        style = {'description_width': '25%'}
+        layout = {'width': '400px'}
+
+        name_button_layout={'width':'25%'}
+        widget_layout = {'width': '15%'}
+        widget_layout_long = {'width': '20%'}
+        units_button_layout ={'width':'15%'}
+        desc_button_layout={'width':'45%'}
+        divider_button_layout={'width':'40%'}
+        divider_button_layout={'width':'60%'}
+        box_layout = Layout(display='flex', flex_flow='row', align_items='stretch', width='100%')
+
+        self.cell_type_dropdown = Dropdown(description='Cell type:',)
+        self.cell_type_dropdown.style = {'description_width': '%sch' % str(len(self.cell_type_dropdown.description) + 1)}
+
+        cell_type_names_layout={'width':'30%'}
+        cell_type_names_style={'description_width':'initial'}
+#        self.parent_name = Text(value='None',description='inherits properties from parent type:',disabled=True, style=cell_type_names_style, layout=cell_type_names_layout)
+
+#        explain_inheritance = Label(value='    This cell line inherits its properties from its parent type. Any settings below override those inherited properties.')  # , style=cell_type_names_style, layout=cell_type_names_layout)
+
+#        self.cell_type_parent_row = HBox([self.cell_type_dropdown, self.parent_name])
+        self.cell_type_parent_row = HBox([self.cell_type_dropdown])
+#        self.cell_type_parent_dict = {}
+"""
+
+
+fill_gui_str= """
+
+    # Populate the GUI widgets with values from the XML
+    def fill_gui(self, xml_root):
+        uep = xml_root.find('.//cell_definitions')  # find unique entry point
+
+"""
+
+fill_xml_str= """
+
+    # Read values from the GUI widgets to enable editing XML
+    def fill_xml(self, xml_root):
+        uep = xml_root.find('.//cell_definitions')  # find unique entry point
+
+"""
+
+display_cell_type_default = """
+    #------------------------------
+    def display_cell_type_default(self):
+        # print("display_cell_type_default():")
+        #print("    self.cell_type_parent_dict = ",self.cell_type_parent_dict)
+
+        # There's probably a better way to do this, but for now,
+        # we hide all vboxes containing the widgets for the different cell defs
+        # and only display the contents of 'default'
+        for vb in self.cell_def_vboxes:
+            vb.layout.display = 'none'   # vs. 'contents'
+        self.cell_def_vboxes[1].layout.display = 'contents'
+"""
+
+cell_type_dropdown_cb = """
+    #------------------------------
+    def cell_type_cb(self, change):
+        if change['type'] == 'change' and change['name'] == 'value':
+            # print("changed to %s" % change['new'])
+            # self.parent_name.value = self.cell_type_parent_dict[change['new']]
+            # idx_selected = list(self.cell_type_parent_dict.keys()).index(change['new'])
+            idx_selected = list(self.cell_type_dict.keys()).index(change['new'])
+            # print('index=',idx_selected)
+            # self.vbox1.layout.visibility = 'hidden'  # vs. visible
+            # self.vbox1.layout.visibility = None 
+
+            # There's probably a better way to do this, but for now,
+            # we hide all vboxes containing the widgets for the different cell defs
+            # and only display the contents of the selected one.
+            for vb in self.cell_def_vboxes:
+                vb.layout.display = 'none'   # vs. 'contents'
+            self.cell_def_vboxes[idx_selected+1].layout.display = 'contents'   # vs. 'contents'  (added "+1" to idx_selected for version 4)
+
+"""
+
+# Now parse a configuration file (.xml) and map the user parameters into GUI widgets
+#tree = ET.parse('../config/PhysiCell_settings.xml')
+try:
+    tree = ET.parse(config_file)
+except:
+    print("Cannot parse",config_file, "- check it's XML syntax.")
+    sys.exit(1)
+
+root = tree.getroot()
+
+indent = "        "
+indent2 = "          "
+widgets = {"double":"FloatText", "int":"IntText", "bool":"Checkbox", "string":"Text", "divider":""}
+#widgets = {"double":"FloatText", "int":"IntText", "bool":"Checkbox", "string":"Text"}
+type_cast = {"double":"float", "int":"int", "bool":"bool", "string":"", "divider":"Text"}
+main_vbox_str = "\n" + indent + "self.tab = VBox([\n"
+#param_desc_buttons_str = "\n" 
+#name_buttons_str = "\n" 
+units_buttons_str = "\n" 
+desc_buttons_str = "\n"
+header_buttons_str = "\n"
+row_str = "\n"
+box_str = "\n" + indent + "box_layout = Layout(display='flex', flex_flow='row', align_items='stretch', width='100%')\n"
+row_header_str = "\n"
+box_header_str = "\n"
+#        box1 = Box(children=row1, layout=box_layout)\n"
+
+float_var_count = 0    # FloatText
+text_var_count = 0    # Text
+bool_var_count = 0     # Checkbox
+text_var_count = 0   
+
+button_widget_name = "name_btn"
+button_widget_units = "units_btn"
+
+divider_count = 0
+color_count = 0
+#param_desc_count = 0
+name_count = 0
+units_count = 0
+
+
+custom_data_widgets = {"double":"FloatText", "int":"IntText", "bool":"Checkbox", "string":"Text", "divider":""}
+custom_data_type_cast = {"double":"float", "int":"int", "bool":"bool", "string":"", "divider":"Text"}
+
+#---------- cell_definitions --------------------
+# TODO: cast attributes to lower case before doing equality tests; perform more testing!
+
+uep = root.find('.//cell_definitions')  # find unique entry point (uep) 
+# fill_gui_str += indent + "uep = xml_root.find('.//cell_definitions')  # find unique entry point\n"
+# fill_xml_str += indent + "uep = xml_root.find('.//cell_definitions')  # find unique entry point\n"
+
+# param_count = 0
+   #param_desc_count = 0
+# name_count = 0
+# units_count = 0
+
+print_vars = False
+print_var_types = False
+
+# colors for some dividers
+lightorange = '#ffde6b'
+
+tag_list = []
+
+row_name = "row"
+def create_row_of_widgets(widget_name_list):
+    global row_name, cells_tab_header
+  # row_name = "row" 
+    # row_str = indent + row_name + " = [" + button_widget_name + ", " + w2 +  ", " + button_widget_units + "]\n"
+    row_str = indent + row_name + " = [" 
+    for w in widget_name_list:
+        row_str +=  w + ", " 
+
+    row_str +=  "]\n" 
+    cells_tab_header += row_str
+
+def create_disabled_button_name(name):
+    global cells_tab_header, color_idx, button_widget_name
+    # # creates "button_widget_name"
+    btn_str = indent + button_widget_name + " = Button(description='" + name + "', disabled=True, layout=name_button_layout)\n"
+    cells_tab_header += btn_str 
+    color_str = indent + button_widget_name + ".style.button_color = '" + colorname[color_idx] + "'\n"
+    cells_tab_header += color_str
+
+def create_disabled_button_units(name):
+    global cells_tab_header, color_idx, button_widget_units 
+    btn_str = indent + button_widget_units + " = Button(description='" + name + "', disabled=True, layout=name_button_layout)\n"
+    cells_tab_header += btn_str 
+    color_str = indent + button_widget_units + ".style.button_color = '" + colorname[color_idx] + "'\n"
+    cells_tab_header += color_str
+
+def get_float_stepsize(val_str):
+    fval_abs = abs(float(val_str))
+    if (fval_abs > 0.0):
+        if (fval_abs > 1.0):  # crop
+            delta_val = pow(10, int(math.log10(fval_abs)) - 1)
+        else:   # round
+            delta_val = pow(10, round(math.log10(fval_abs)) - 1)
+    else:
+        delta_val = 0.01  # if initial value=0.0, we're totally guessing at what a good delta is
+    return delta_val
+
+def create_checkbox_widget(name, desc, val):
+    global cells_tab_header, indent
+    toggle_str = indent + name + " = Checkbox(description='" + desc + "', value=" + val + ",layout=name_button_layout)\n"
+    cells_tab_header += toggle_str
+    # return widget_str
+
+def create_float_text_widget(name, initial_val, delta_val):
+    global cells_tab_header, indent, indent2
+    if delta_val > 0:
+        step_val = delta_val
+    else:
+        step_val = get_float_stepsize(str(initial_val))
+    name = name.replace('-','_')
+    # cells_tab_header += "------------ create_float_text_widget(), name=  " + name + "\n"
+    widget_str = indent + name + " = FloatText(value='" + initial_val + "', step='" + str(step_val) + "', style=style, layout=widget_layout)\n"
+    # step=0.1,
+    return widget_str
+
+def create_text_widget(name, str_val):
+    # substrate_text_str = indent + substrate_name + " = Text(value='" + elm.attrib['name'] + "', disabled=False, style=style, layout=widget_layout)\n"
+    widget_str = indent + name + " = Text(value='" + str_val + "', disabled=False, style=style, layout=widget_layout_long)\n"
+    return widget_str
+
+# function to process a "divider" type element
+def handle_divider(child):
+    global divider_count, cells_tab_header, indent, indent2, main_vbox_str
+    divider_count += 1
+    # print('-----------> handler_divider: ',divider_count)
+    divrow_name = "div_row" + str(divider_count)
+    cells_tab_header += "\n" + indent + divrow_name + " = " + "Button(description='" + child.attrib['description'] + "', disabled=True, layout=divider_button_layout)\n"
+    main_vbox_str += indent2 + divrow_name + ",\n"
+
+def handle_divider_pheno(div_str):
+    global divider_count, cells_tab_header, indent, indent2, main_vbox_str
+    divider_count += 1
+    # print('-----------> handler_divider_pheno: ',divider_count)
+    divrow_name = "div_row" + str(divider_count)
+    cells_tab_header += indent + "#  ------------------------- \n"
+    cells_tab_header += indent + divrow_name + " = " + "Button(description='" + div_str + "', disabled=True, layout=divider_button_layout)\n"
+    cells_tab_header += indent + divrow_name + ".style.button_color = 'orange'\n"
+    return divrow_name
+
+# default is to assume "float"
+def fill_gui_and_xml(widget_name, xml_elm):
+    global fill_gui_str, fill_xml_str
+    fill_gui_str += indent + widget_name + ".value = float(uep.find('" + xml_elm + "').text)\n"
+    fill_xml_str += indent + "uep.find('" + xml_elm + "').text = str(" + widget_name + ".value)\n"
+
+def fill_gui_and_xml_bool_attrib(widget_name, xml_elm, attrib_name):
+    global fill_gui_str, fill_xml_str
+    # fill_gui_str += indent + widget_name + ".value = ('true' == (uep.find('" + xml_elm + "').text.lower()))\n"
+    fill_gui_str += indent + widget_name + ".value = ('true' == (uep.find('" + xml_elm + "').attrib['" + attrib_name + "'].lower()))\n"
+
+    # fill_xml_str += indent + "uep.find('" + xml_elm + "').text = str(" + widget_name + ".value)\n"
+    fill_xml_str += indent + "uep.find('" + xml_elm + "').attrib['" + attrib_name + "'] = str(" + widget_name + ".value)\n"
+
+def fill_gui_and_xml_bool(widget_name, xml_elm):
+    global fill_gui_str, fill_xml_str
+    # self.fix_persistence.value = ('true' == (uep.find('.//fix_persistence').text.lower()) )
+    # fill_gui_str += indent + widget_name + ".value = ('true' == (uep.find('" + xml_elm + "').text.lower()))\n"
+    fill_gui_str += indent + widget_name + ".value = ('true' == (uep.find('" + xml_elm + "').text.lower()))\n"
+
+    # uep.find('.//fix_persistence').text = str(self.fix_persistence.value)
+    # fill_xml_str += indent + "uep.find('" + xml_elm + "').text = str(" + widget_name + ".value)\n"
+    fill_xml_str += indent + "uep.find('" + xml_elm + "').text = str(" + widget_name + ".value)\n"
+
+def fill_gui_and_xml_string(widget_name, xml_elm):
+    global fill_gui_str, fill_xml_str
+    fill_gui_str += indent + widget_name + ".value = uep.find('" + xml_elm + "').text\n"
+    fill_xml_str += indent + "uep.find('" + xml_elm + "').text = str(" + widget_name + ".value)\n"
+
+def fill_gui_and_xml_string_attrib(widget_name, xml_elm, attrib_name):
+    global fill_gui_str, fill_xml_str
+    fill_gui_str += indent + widget_name + ".value = uep.find('" + xml_elm + "').attrib['" + attrib_name + "']\n"
+    # fill_xml_str += indent + "uep.find('" + xml_elm + "').text = str(" + widget_name + ".value)\n"
+    fill_xml_str += indent + "uep.find('" + xml_elm + "').attrib['" + attrib_name + "'] = str(" + widget_name + ".value)\n"
+
+
+def fill_gui_and_xml_comment(s):
+    global fill_gui_str, fill_xml_str
+    fill_gui_str += indent + s + "\n"
+    fill_xml_str += indent + s + "\n"
+
+#===========  main loop ===================
+ndent = "\n" + indent 
+ndent2 = "\n" + indent2
+
+# NOTE: we assume a simple "children-only" hierarchy in <user_parameters>
+# for child in uep:   # uep = "unique entry point" for <user_parameters> (from above)
+
+#        self.cell_type.options={'default':'default', 'worker':'worker', 'director':'director', 'cargo':'cargo'}
+cells_tab_header += ndent + "self.cell_type_dict = {}"  
+#row_name + " = " + "Button(description='" + child.attrib['description'] + "', disabled=True, layout=divider_button_layout)\n"
+
+
+#--------- Let's do a 3-pass parsing of <cell_definitions> in the .xml file
+
+#--- 1) create a dict ("cell_type_dict") of <cell_definition> names
+for child in uep.findall('cell_definition'):
+    if print_vars:
+        print(child.tag, child.attrib)
+        print(child.attrib['name'])
+    # cells_tab_header += "'" + child.attrib['name'] + ":'"
+    if child.attrib['name'] != 'default':   # version 4: don't include 'default' in dropdown widget
+        name_str = "'" + child.attrib['name'] + "'"
+        cells_tab_header += ndent + "self.cell_type_dict[" + name_str + "] = " + name_str 
+
+cells_tab_header += ndent + "self.cell_type_dropdown.options = self.cell_type_dict\n"
+cells_tab_header += ndent + "self.cell_type_dropdown.observe(self.cell_type_cb)\n"
+            
+#--- 2) create a dict ("cell_type_parent_dict") of <cell_definition> parents
+# for child in uep.findall('cell_definition'):
+#     name_str = "'" + child.attrib['name'] + "'"
+#     if 'parent_type' in child.attrib:
+#         parent_str = "'" + child.attrib['parent_type'] + "'"
+#     else:
+#         parent_str = "'None'"
+#     cells_tab_header += ndent + "self.cell_type_parent_dict[" + name_str + "] = " + parent_str 
+# cells_tab_header += "\n\n"
+# e.g., self.cell_type_parent_dict =  {'default': 'None', 'lung epithelium': 'default', 'immune': 'default', 'CD8 Tcell': 'immune', 'macrophage': 'immune', 'neutrophil': 'immune'}
+
+
+#main_vbox_str += indent2 + "self.cell_type_parent_row, explain_inheritance, \n"
+main_vbox_str += indent2 + "self.cell_type_parent_row,  \n"
+#    cells_tab_header += "\n" + indent + row_name + " = " + "Button(description='" + child.attrib['description'] + "', disabled=True, layout=divider_button_layout)\n"
+
+
+cells_tab_header += ndent + "self.cell_def_vboxes = []\n" 
+
+motility_count = 0
+cell_def_count = 0
+box_count = 0
+
+#--- 3) primary pass to generate all ipywidgets Python code, initialize their values from those 
+#       in the .xml, and generate code for the 2 functions, "fill_gui" and "fill_xml"
+#       
+for cell_def in uep.findall('cell_definition'):
+    color_idx = 0
+    cell_def_name = cell_def.attrib['name']
+    uep_phenotype = cell_def.find('phenotype')  # cell_def children: currently just <phenotype> and <custom_data> 
+
+    cells_tab_header += indent + "#  >>>>>>>>>>>>>>>>> <cell_definition> = " + cell_def.attrib['name'] + "\n"
+
+    subpath0 = ".//cell_definition[" + str(cell_def_count+1) + "]" + "//phenotype"
+
+    print("\n---------------- subpath0 ",cell_def.attrib['name'], " = ", subpath0)
+    fill_gui_and_xml_comment("# ------------------ cell_definition: " + cell_def.attrib['name'])
+
+    #   print('pheno=',uep_phenotype)
+    prefix = 'phenotype:'
+
+    elm_str = ""   # element string: this will contain all widget names that go into this cell def VBox
+
+    rate_count = 0
+    for child in uep_phenotype:
+        print('pheno child=',child)
+        if child.tag == 'cycle':  # <cycle code="6" name="flow_cytometry_separated_cycle_model">
+            cycle_name = ""
+            if 'name' in child.attrib.keys():   
+                cycle_name = child.attrib['name']
+
+            cycle_code = ""
+            if 'code' in child.attrib.keys():   
+                cycle_code = child.attrib['code']
+
+            fill_gui_and_xml_comment("# ---------  cycle (" + cycle_name + ")")  
+
+            subpath1 = subpath0  + "//" + child.tag
+
+            # print('cycle code=',child.attrib['code'])
+            # print('cycle name=',child.attrib['name'])
+
+            divider_pheno_name = handle_divider_pheno(prefix + child.tag + " (model: " + cycle_name + "; code=" + cycle_code + ")" ) 
+            elm_str += divider_pheno_name + ", "
+            # print(elm_str)
+            color_str = indent + divider_pheno_name + ".style.button_color = '" + colorname[color_idx] + "'\n"
+
+            # <phase_durations units="min"> 
+            #     <duration index="0" fixed_duration="false">300.0</duration>
+            for cycle_child in child:
+                if cycle_child.tag == 'phase_durations':
+                    subpath2 = subpath1 +  "//phase_durations"
+                    units_str = ""
+                    if 'units' in cycle_child.attrib.keys():
+                        units_str = cycle_child.attrib['units']
+                    duration_count = 0
+                    for duration_elm in cycle_child:
+                        w0 = "self.bool" + str(bool_var_count)
+                        bool_var_count += 1
+
+                        duration_count += 1
+                        subpath3 = subpath2 +  "//duration[" + str(duration_count) + "]"
+
+                        if duration_elm.attrib['fixed_duration'].lower() == 'true':
+                            val = "True"
+                        else:
+                            val = "False"
+                        attrib_name = 'fixed_duration'
+                        toggle_str = indent + w0 + " = Checkbox(description='" + attrib_name + "', value=" + val + ",layout=name_button_layout)\n"
+                        cells_tab_header += toggle_str
+                        # create_checkbox_widget(w0, attrib_name, val)
+
+                        fill_gui_and_xml_bool_attrib(w0, subpath3, attrib_name)
+
+                        btn_name = "duration"
+                        create_disabled_button_name(btn_name)  # creates "button_widget_name"
+
+                        w2 = "self.float" + str(float_var_count)
+                        float_var_count += 1
+                        cells_tab_header += create_float_text_widget(w2, duration_elm.text, -1)
+
+                        fill_gui_and_xml(w2,subpath3)
+
+                        create_disabled_button_units(units_str)  # creates "button_widget_units"
+                        color_idx = 1 - color_idx
+
+                        create_row_of_widgets([w0, button_widget_name, w2, button_widget_units])
+
+                        box_name = "box" + str(box_count) 
+                        box_count += 1
+                        box_str = indent + box_name + " = Box(children=" + row_name + ", layout=box_layout)\n\n"
+                        cells_tab_header += box_str 
+                        elm_str += box_name + ", "
+
+
+                elif cycle_child.tag == 'phase_transition_rates':
+                    subpath2 = subpath1 + "//" + cycle_child.tag
+                    # print("\n---------------- subpath2 = ", subpath2)
+                    for rates in child:
+                        units_str = ""
+                        if 'units' in rates.attrib.keys():
+                            units_str = rates.attrib['units']
+                        rate_count = 0
+                        for rate in rates:
+                            # btn_name = "transition rate: " + rate.attrib['start_index'] + "->" + rate.attrib['end_index']
+                            btn_name = "Phase " + rate.attrib['start_index'] + " -> Phase " + rate.attrib['end_index'] + " transition rate"
+                            create_disabled_button_name(btn_name)  # creates "button_widget_name"
+
+                            w2 = "self.float" + str(float_var_count)
+                            float_var_count += 1
+                            cells_tab_header += create_float_text_widget(w2, rate.text, -1)
+
+                            rate_count += 1
+
+                            subpath = subpath2 +  "//rate[" + str(rate_count) + "]"
+
+                            fill_gui_and_xml(w2, subpath)
+
+                            create_disabled_button_units(units_str)  # creates "button_widget_units"
+                            color_idx = 1 - color_idx
+
+                            # row_name = "row" 
+                            # row_str = indent + row_name + " = [" + button_widget_name + ", " + w2 +  ", " + button_widget_units + "]\n"
+                            # cells_tab_header += row_str
+                            create_row_of_widgets([button_widget_name, w2, button_widget_units])
+
+                            box_name = "box" + str(box_count) 
+                            box_count += 1
+                            box_str = indent + box_name + " = Box(children=" + row_name + ", layout=box_layout)\n\n"
+                            cells_tab_header += box_str 
+                            elm_str += box_name + ", "
+
+
+        elif child.tag == 'death':
+            fill_gui_and_xml_comment("# ---------  death ") 
+
+            subpath1 = subpath0  + "//" + child.tag
+            death_model_count = 0
+            elm_str += handle_divider_pheno(prefix + child.tag) + ", "
+            for death_model in child:
+                death_model_count += 1
+                subpath2 = subpath1 +  "//model[" + str(death_model_count) + "]"
+
+                death_row_name = "death_model" + str(death_model_count)
+                death_header_str = indent + death_row_name + " = " + "Button(description='model: " + death_model.attrib['name'] + "', disabled=True, layout={'width':'30%'})\n"
+                cells_tab_header += death_header_str 
+                cells_tab_header += indent + death_row_name + ".style.button_color = '" + lightorange + "'\n" 
+                elm_str += death_row_name + ","
+
+                # print('death code=',death_model.attrib['code'])
+                # print('death name=',death_model.attrib['name'])
+
+                #----------  overall death model rate -------------
+                rate = death_model.find('.//death_rate')  
+                subpath3 = subpath2 +  "//death_rate"
+
+                create_disabled_button_name("death rate")  # creates "button_widget_name"
+
+                w2 = "self.float" + str(float_var_count)
+                float_var_count += 1
+                cells_tab_header += create_float_text_widget(w2, rate.text, -1)
+
+                create_disabled_button_units(units_str)  # creates "button_widget_units"
+                color_idx = 1 - color_idx
+
+                fill_gui_and_xml(w2, subpath3)
+