xml2jupyter.py

#
# Parse a PhysiCell configuration file (XML) and generate a Jupyter (Python) module (user_params.py)
# containing associated widgets for user parameters.
#
# Authors: Randy Heiland, Daniel Mishler, Tyler Zhang, Eric Bower, and Paul Macklin
#
import sys
import math
import xml.etree.ElementTree as ET

num_args = len(sys.argv)
print("num_args=",num_args)
if ( num_args < 2):
#    print("Usage: python " + sys.argv[0] + " <config-file.xml> [<gui-file.py>]")
    print("Usage: python " + sys.argv[0] + " <config-file.xml> [<gui-file.py>] [<colorname1>] [<colorname2>]")
    sys.exit(1)
config_file = sys.argv[1]
colorname1 = 'lightgreen'
colorname2 = 'tan'

if ( num_args == 3):
    gui_file = sys.argv[2]
elif ( num_args ==4 ):
    print("Usage: python " + sys.argv[0] + " <config-file.xml> <gui-file.py> <colorname1> <colorname2>")
    sys.exit(1)
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)

# First, let's use this config file name in the (main) mygui.py module:
# f_main = open('mygui.py', 'r')
# for line in f_main:
#     if 'full_xml_filename' in line:
#         print(line)
# #        break
#         sys.exit(1)
if (num_args == 3):
#    with open('mygui.py') as f:
    with open(gui_file) as f:
    #  newText = f.read().replace('myconfig.xml', config_file) # rwh 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('mygui.py', "w") as f:
    with open(gui_file, "w") as f:
        f.write(file_pre)
        f.write("main_xml_filename = '" + config_file + "'")
        f.write(file_post)

user_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
    
class UserTab(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%'}
        units_button_layout ={'width':'15%'}
        desc_button_layout={'width':'45%'}
"""

"""
        self.therapy_activation_time = BoundedFloatText(
            min=0.,
            max=100000000,
            step=stepsize,
            description='therapy_activation_time',
            style=style, layout=layout,
            # layout=Layout(width=constWidth),
        )
        self.save_interval_after_therapy_start = BoundedFloatText(
            min=0.,
            max=100000000,
            step=stepsize,
            description='save_interval_after_therapy_start',
            style=style, layout=layout,
        )

        label_blankline = Label('')

        self.tab = VBox([HBox([self.therapy_activation_time, Label('min')]), 
                         HBox([self.save_interval_after_therapy_start, Label('min')]), 
                         ])  
"""

fill_gui_str= """

    # Populate the GUI widgets with values from the XML
    def fill_gui(self, xml_root):
        uep = xml_root.find('.//user_parameters')  # find unique entry point into XML
"""

fill_xml_str= """

    # Read values from the GUI widgets to enable editing XML
    def fill_xml(self, xml_root):
        uep = xml_root.find('.//user_parameters')  # find unique entry point into XML 
"""

# Now parse a configuration file (.xml) and map the user parameters into GUI widgets
#tree = ET.parse('../config/PhysiCell_settings.xml')
tree = ET.parse(config_file)
root = tree.getroot()
uep = root.find('.//user_parameters')  # find unique entry point (uep) to user params
indent = "        "
indent2 = "          "
widgets = {"double":"FloatText", "int":"IntText", "bool":"Checkbox", "string":"Text"}
type_cast = {"double":"float", "int":"int", "bool":"bool", "string":""}
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" 
row_str = "\n"
box_str = "\n" + indent + "box_layout = Layout(display='flex', flex_flow='row', align_items='stretch', width='100%')\n"

#        box1 = Box(children=row1, layout=box_layout)\n"

# TODO: cast attributes to lower case before doing equality tests; perform more testing!

param_count = 0
#param_desc_count = 0
name_count = 0
units_count = 0

tag_list = []
for child in uep:
    print(child.tag, child.attrib)
    if child.tag in tag_list:
        print("-------> Warning: duplicate tag!  ", child.tag)
        continue
    else:
        tag_list.append(child.tag)
    units_str = ""
    describe_str = ""
    if 'hidden' in child.attrib.keys() and (child.attrib['hidden'].lower() == "true"):   # do we want to hide this from the user?
        print("  HIDE this parameter from the GUI: ", child.tag)
        continue

#    names_str = ''
#    units_str = ''
    describe_str = ''
#    desc_row_name = None
    desc_row_name = ''
    units_btn_name = ''
    param_count += 1
    if 'description' in child.attrib.keys():
        describe_str = child.attrib['description']
    else:
        describe_str = ""
    desc_row_name = "desc_button" + str(param_count)
    desc_buttons_str += indent + desc_row_name + " = " + "Button(description='" + describe_str + "', disabled=True, layout=desc_button_layout) \n"
    if (param_count % 2):
        desc_buttons_str += indent + desc_row_name + ".style.button_color = '" + colorname1 + "'\n"
    else:  # rf.  https://www.w3schools.com/colors/colors_names.asp
        desc_buttons_str += indent + desc_row_name + ".style.button_color = '" + colorname2 + "'\n"

    if 'units' in child.attrib.keys():
        if child.attrib['units'] != "dimensionless" and child.attrib['units'] != "none":
#            units_str = child.attrib['units']
            units_count += 1
            units_btn_name = "units_button" + str(units_count)
            units_buttons_str += indent + units_btn_name + " = " + "Button(description='" + child.attrib['units'] + "', disabled=True, layout=units_button_layout) \n"
            if (param_count % 2):
                units_buttons_str += indent + units_btn_name + ".style.button_color = '" + colorname1 + "'\n"
            else:  # rf.  https://www.w3schools.com/colors/colors_names.asp
                units_buttons_str += indent + units_btn_name + ".style.button_color = '" + colorname2 + "'\n"
        else:
            units_count += 1
            units_btn_name = "units_button" + str(units_count)
            units_buttons_str += indent + units_btn_name + " = " + "Button(description='" +  "', disabled=True, layout=units_button_layout) \n"
            if (param_count % 2):
                units_buttons_str += indent + units_btn_name + ".style.button_color = '" + colorname1 + "'\n"
            else:  # rf.  https://www.w3schools.com/colors/colors_names.asp
                units_buttons_str += indent + units_btn_name + ".style.button_color = '" + colorname2 + "'\n"
    else:
        units_count += 1
        units_btn_name = "units_button" + str(units_count)
        units_buttons_str += indent + units_btn_name + " = " + "Button(description='" +  "', disabled=True, layout=units_button_layout) \n"
        if (param_count % 2):
            units_buttons_str += indent + units_btn_name + ".style.button_color = '" + colorname1 + "'\n"
        else:  # rf.  https://www.w3schools.com/colors/colors_names.asp
            units_buttons_str += indent + units_btn_name + ".style.button_color = '" + colorname2 + "'\n"

    if 'type' in child.attrib.keys():
#             self.therapy_activation_time = BoundedFloatText(
#            min=0., max=100000000, step=stepsize,
        full_name = "self." + child.tag
        name_count += 1
        if child.attrib['type'] not in widgets.keys():
            print("    *** Error - Invalid type: " + child.attrib['type'])
            sys.exit(1)
        else:    
            param_name_button = "param_name" + str(name_count)
            user_tab_header += "\n" + indent + param_name_button + " = " + "Button(description='" + child.tag + "', disabled=True, layout=name_button_layout)\n"
            if (param_count % 2):
                user_tab_header += indent + param_name_button + ".style.button_color = '" + colorname1 + "'\n"
            else:  # rf.  https://www.w3schools.com/colors/colors_names.asp
                user_tab_header += indent + param_name_button + ".style.button_color = '" + colorname2 + "'\n"
            user_tab_header += "\n" + indent + full_name + " = " + widgets[child.attrib['type']] + "(\n"

            # Try to calculate and provide a "good" delta step (for the tiny "up/down" arrows on a numeric widget)
            if child.attrib['type'] == "double":
                fval_abs = abs(float(child.text))
                if (fval_abs > 0.0):
                    if (fval_abs > 1.0):  # crop
                        delta_val = pow(10, int(math.log10(abs(float(child.text)))) - 1)
                    else:   # round
                        delta_val = pow(10, round(math.log10(abs(float(child.text)))) - 1)
                else:
                    delta_val = 0.01  # if initial value=0.0, we're totally guessing at what a good delta is
                print('double: ',float(child.text),', delta_val=',delta_val)

                user_tab_header += indent2 + "value=" + child.text + ",\n"
                # Note: "step" values will advance the value to the nearest multiple of the step value itself :-/
                user_tab_header += indent2 + "step=" + str(delta_val) + ",\n"

            # Integers
            elif child.attrib['type'] == "int":  # warning: math.log(1000,10)=2.99..., math.log10(1000)=3  
                if (abs(int(child.text)) > 0):
                    delta_val = pow(10,int(math.log10(abs(int(child.text)))) - 1)
                else:
                    delta_val = 1  # if initial value=0, we're totally guessing at what a good delta is
                print('int: ',int(child.text),', delta_val=',delta_val)

                user_tab_header += indent2 + "value=" + child.text + ",\n"
                user_tab_header += indent2 + "step=" + str(delta_val) + ",\n"

            # Booleans
            elif child.attrib['type'] == "bool":
                if (child.text.lower() == "true"):
                    child.text = "True"
                elif (child.text.lower() == "false"):
                    child.text = "False"
                else:
                    print(" --- ERROR: bool must be True or False, not ", child.text)
                    sys.exit(1)

                print('bool: ',child.text)
                user_tab_header += indent2 + "value=" + child.text + ",\n"
            
            # Strings
            elif child.attrib['type'] == "string":
                user_tab_header += indent2 + "value='" + child.text + "',\n"


            # Finally, append the info at the end of this widget
            user_tab_header += indent2 + "style=style, layout=widget_layout)\n"

            row_name = "row" + str(param_count)
            row_str += indent +  row_name + " = [" + param_name_button + ", " + full_name + ", " + units_btn_name + ", " + desc_row_name + "] \n"
            box_name = "box" + str(param_count)
            box_str += indent + box_name + " = Box(children=" + row_name + ", layout=box_layout)\n"
            vbox_str += indent2 + box_name + ",\n"

            # float, int, bool
            if (type_cast[child.attrib['type']] == "bool"):
                fill_gui_str += indent + full_name + ".value = ('true' == (uep.find('.//" + child.tag + "').text.lower()) )\n"
            else:
                fill_gui_str += indent + full_name + ".value = " + type_cast[child.attrib['type']] + "(uep.find('.//" + child.tag + "').text)\n"

            fill_xml_str += indent + "uep.find('.//" + child.tag + "').text = str("+ full_name + ".value)\n"

vbox_str += indent + "])"

# Write the beginning of the Python module for the user parameters tab in the GUI
user_tab_file = "user_params.py"
print("\n --------------------------------- ")
print("Generated a new: ", user_tab_file)
print()
#print("If this is your first time:")
#print("Run the GUI via:  jupyter notebook mygui.ipynb")
print("Test the minimal GUI via:  jupyter notebook test_gui.ipynb")
print("run the Jupyter menu item:  Cell -> Run All")
print()
print("(or, if you already have a previous GUI running and want to see new params:")
print("run the Jupyter menu item:  Kernel -> Restart & Run All)")
print()
fp= open(user_tab_file, 'w')
fp.write(user_tab_header)
fp.write(units_buttons_str)
fp.write(desc_buttons_str)
fp.write(row_str)
fp.write(box_str)
fp.write(vbox_str)
fp.write(fill_gui_str)
fp.write(fill_xml_str)
fp.close()