initial commit

.travis.yml

+# Enable C++ support
+language: cpp
+
+os: linux
+
+# Compiler selection
+compiler:
+  - gcc
+
+# Build steps
+script:
+  - cd src
+  - make
+
+notifications:
+  email:
+    recipients:
+      - randy.heiland@gmail.com
+    on_success: always # default: change  (always, never)
+    on_failure: always # default: always

LICENSE

+BSD 3-Clause License
+
+Copyright (c) 2019, PhysiCell-Tools
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

-# pc4covid19
-PhysiCell for COVID19 simulator app for nanoHUB
+# pc4covid19 - COVID19 tissue simulator nanoHUB app
+
+**Version:** 1.0
+
+**Release date:** 26 March 2020 
+
+This repository contains code and data for the nanoHUB app https://nanohub.org/tools/pc4covid19
+
+### Refererences
+https://github.com/MathCancer/COVID19
+
+https://github.com/MathCancer/COVID19/wiki/About

bin/about.py

+from ipywidgets import Output
+from IPython.display import display, HTML
+
+class AboutTab(object):
+
+    def __init__(self):
+        # self.tab = Output(layout={'height': '600px'})
+        self.tab = Output(layout={'height': 'auto'})
+        self.tab.append_display_data(HTML(filename='doc/about.html'))
+        

bin/animate_tab.py

+from ipywidgets import Button, VBox, Output
+from IPython.display import display, HTML
+import os
+import glob
+import subprocess
+import time
+
+class AnimateTab(object):
+
+    def __init__(self):
+        # self.tab = Output(layout={'height': '600px'})
+        # self.tab = Output(layout={'height': 'auto'})
+
+        gen_button = Button(
+            description='Generate',
+            button_style='success',  # 'success', 'info', 'warning', 'danger' or ''
+            tooltip='Generate a MP4 video of cells',
+        )
+        gen_button.on_click(self.gen_button_cb)
+
+        animate_out = Output(layout={'height': 'auto'})
+        animate_out.append_display_data(HTML(filename='doc/animate.html'))
+
+        self.tab = VBox([gen_button, animate_out])
+
+    def gen_button_cb(self, b):
+        print('running...')
+        tdir = os.path.abspath('tmpdir')
+        os.chdir(tdir)
+    # os.system('rm -rf tmpdir*')
+    # subprocess.Popen(["../bin/myproj", "config.xml"])
+        # cmd = 'magick mogrify -format jpg snapshot*.svg'
+        # print(cmd)
+        # os.system(cmd)
+        # cmd = 'mencoder "mf://snapshot*.jpg" -ovc lavc -lavcopts vcodec=mpeg4:vbitrate=10000:mbd=2:trell -mf fps=5:type=jpg -nosound -o out.avi'
+        # print(cmd)
+        # os.system(cmd)
+        # cmd = 'convert out.avi cells.mp4'
+        # print(cmd)
+        # os.system(cmd)
+        # print('done.')
+
+
+        num_svg = len(glob.glob('snap*.svg'))
+        idx_start = 0
+        idx_end = num_svg
+        for idx in range(idx_start,idx_end):
+            fname = "snapshot%08d" % idx
+            # cmd = "convert " + fname + ".svg -resize " + str(resize_pct) + "% " + fname + ".jpg &" 
+            svg_file = fname + ".svg"
+            jpg_file = fname + ".jpg"
+            # print("convert " + svg_file + " " + jpg_file)
+            # print(cmd)
+            #  os.system(cmd)
+            # subprocess.Popen(["../bin/myproj", "config.xml"])
+            subprocess.Popen(["convert", svg_file, jpg_file])
+        print("Converting all svg to jpg...")
+
+        delay = 15  # secs
+        # while True:
+        for idx in range(num_svg):
+            print ("%s" % ( time.ctime(time.time()) ))
+            # print(len(glob.glob(os.path.join(".", 'snap*.svg'))))
+            num_jpg = len(glob.glob('snap*.jpg'))
+            print("%d of %d" % (num_jpg, num_svg))
+            time.sleep(delay)
+            if num_jpg == num_svg:
+                break
+
+        cmd = 'mencoder "mf://snapshot*.jpg" -ovc lavc -lavcopts vcodec=mpeg4:vbitrate=10000:mbd=2:trell -mf fps=5:type=jpg -nosound -o out.avi'
+        print(cmd)
+        os.system(cmd)
+        cmd = 'convert out.avi cells.mp4'
+        print(cmd)
+        os.system(cmd)
+        print('done.')
+
+        # %%HTML
+# <video width=500 height=500 controls>
+#   <source src="out.mp4" type="video/mp4">
+# </video>
+
+        

bin/config.py

+# Config Tab
+
+import os
+from ipywidgets import Layout, Label, Text, Checkbox, Button, HBox, VBox, \
+    FloatText, BoundedIntText, BoundedFloatText, HTMLMath, Dropdown
+
+
+class ConfigTab(object):
+
+    def __init__(self):
+        
+#        micron_units = HTMLMath(value=r"$\mu M$")
+        micron_units = Label('micron')   # use "option m" (Mac, for micro symbol)
+#        micron_units = Label('microns')   # use "option m" (Mac, for micro symbol)
+
+        constWidth = '180px'
+        # tab_height = '400px'
+        tab_height = '500px'
+#        tab_layout = Layout(width='900px',   # border='2px solid black',
+#        tab_layout = Layout(width='850px',   # border='2px solid black',
+#                            height=tab_height, overflow_y='scroll',)
+#        np_tab_layout = Layout(width='800px',  # border='2px solid black',
+#                               height='350px', overflow_y='scroll',)
+
+        # my_domain = [0,0,-10, 2000,2000,10, 20,20,20]  # [x,y,zmin,  x,y,zmax, x,y,zdelta]
+#        label_domain = Label('Domain ($\mu M$):')
+        label_domain = Label('Domain (micron):')
+        stepsize = 10
+        disable_domain = False
+        self.xmin = FloatText(step=stepsize,
+            # description='$X_{min}$',
+            description='Xmin',
+            disabled = disable_domain,
+            layout=Layout(width=constWidth),
+        )
+        self.ymin = FloatText(step=stepsize,
+            description='Ymin',
+            disabled = disable_domain,
+            layout=Layout(width=constWidth),
+        )
+        self.zmin = FloatText(step=stepsize,
+            description='Zmin',
+            disabled = disable_domain,
+            layout=Layout(width=constWidth),
+        )
+        self.xmax = FloatText(step=stepsize,
+            description='Xmax',
+            disabled = disable_domain,
+            layout=Layout(width=constWidth),
+        )
+        self.ymax = FloatText(step=stepsize,
+            description='Ymax',
+            disabled = disable_domain,
+            layout=Layout(width=constWidth),
+        )
+        self.zmax = FloatText(step=stepsize,
+            description='Zmax',
+            disabled = disable_domain,
+            layout=Layout(width=constWidth),
+        )
+#            description='$Time_{max}$',
+        self.tmax = BoundedFloatText(
+            min=0.,
+            max=100000000,
+            step=stepsize,
+            description='Max Time',
+            layout=Layout(width=constWidth),
+        )
+        self.xdelta = BoundedFloatText(
+            min=1.,
+            description='dx',   # '∆x',  # Mac: opt-j for delta
+            disabled = disable_domain,
+            layout=Layout(width=constWidth),
+        )
+
+
+        self.ydelta = BoundedFloatText(
+            min=1.,
+            description='dy',
+            disabled = True,
+            layout=Layout(width=constWidth),
+        )
+        self.zdelta = BoundedFloatText(
+            min=1.,
+            description='dz',
+            disabled = disable_domain,
+            layout=Layout(width=constWidth),
+        )
+
+        def xdelta_cb(b):
+            self.ydelta.value = self.xdelta.value
+            self.zdelta.value = 0.5 * (self.xdelta.value + self.ydelta.value)
+            self.zmin.value = -0.5 * self.zdelta.value 
+            self.zmax.value = 0.5 * self.zdelta.value 
+
+        self.xdelta.observe(xdelta_cb)  
+
+
+        """
+        self.tdelta = BoundedFloatText(
+            min=0.01,
+            description='$Time_{delta}$',
+            layout=Layout(width=constWidth),
+        )
+        """
+
+        """
+        self.toggle2D = Checkbox(
+            description='2-D',
+            layout=Layout(width=constWidth),
+        )
+        def toggle2D_cb(b):
+            if (self.toggle2D.value):
+                #zmin.disabled = zmax.disabled = zdelta.disabled = True
+                zmin.disabled = True
+                zmax.disabled = True
+                zdelta.disabled = True
+            else:
+                zmin.disabled = False
+                zmax.disabled = False
+                zdelta.disabled = False
+            
+        self.toggle2D.observe(toggle2D_cb)
+        """
+
+        x_row = HBox([self.xmin, self.xmax, self.xdelta])
+        y_row = HBox([self.ymin, self.ymax, self.ydelta])
+        z_row = HBox([self.zmin, self.zmax, self.zdelta])
+
+        self.omp_threads = BoundedIntText(
+            min=1,
+            max=4,
+            description='# threads',
+            layout=Layout(width=constWidth),
+        )
+
+        # self.toggle_prng = Checkbox(
+        #     description='Seed PRNG', style={'description_width': 'initial'},  # e.g. 'initial'  '120px'
+        #     layout=Layout(width=constWidth),
+        # )
+        # self.prng_seed = BoundedIntText(
+        #     min = 1,
+        #     description='Seed', 
+        #     disabled=True,
+        #     layout=Layout(width=constWidth),
+        # )
+        # def toggle_prng_cb(b):
+        #     if (toggle_prng.value):
+        #         self.prng_seed.disabled = False
+        #     else:
+        #         self.prng_seed.disabled = True
+            
+        # self.toggle_prng.observe(toggle_prng_cb)
+        #prng_row = HBox([toggle_prng, prng_seed])
+
+        self.toggle_svg = Checkbox(
+            description='Cells',    # SVG
+            layout=Layout(width='150px') )  # constWidth = '180px'
+        # self.svg_t0 = BoundedFloatText (
+        #     min=0,
+        #     description='$T_0$',
+        #     layout=Layout(width=constWidth),
+        # )
+        self.svg_interval = BoundedIntText(
+            min=1,
+            max=99999999,   # TODO: set max on all Bounded to avoid unwanted default
+            description='every',
+            layout=Layout(width='160px'),
+        )
+        self.mcds_interval = BoundedIntText(
+            min=1,
+            max=99999999,
+            description='every',
+#            disabled=True,
+            layout=Layout(width='160px'),
+        )
+
+        # don't let this be > mcds interval
+        def svg_interval_cb(b):
+            if (self.svg_interval.value > self.mcds_interval.value):
+                self.svg_interval.value = self.mcds_interval.value
+
+        self.svg_interval.observe(svg_interval_cb)  # BEWARE: when fill_gui, this sets value = 1 !
+
+        # don't let this be < svg interval
+        def mcds_interval_cb(b):
+            if (self.mcds_interval.value < self.svg_interval.value):
+                self.mcds_interval.value = self.svg_interval.value
+
+        self.mcds_interval.observe(mcds_interval_cb)   # BEWARE: see warning above
+
+        def toggle_svg_cb(b):
+            if (self.toggle_svg.value):
+                # self.svg_t0.disabled = False 
+                self.svg_interval.disabled = False
+            else:
+                # self.svg_t0.disabled = True
+                self.svg_interval.disabled = True
+            
+        self.toggle_svg.observe(toggle_svg_cb)
+
+
+        self.toggle_mcds = Checkbox(
+        #     value=False,
+            description='Subtrates',   # Full
+            layout=Layout(width='180px'),
+        )
+        # self.mcds_t0 = FloatText(
+        #     description='$T_0$',
+        #     disabled=True,
+        #     layout=Layout(width=constWidth),
+        # )
+        def toggle_mcds_cb(b):
+            if (self.toggle_mcds.value):
+                # self.mcds_t0.disabled = False #False
+                self.mcds_interval.disabled = False
+            else:
+                # self.mcds_t0.disabled = True
+                self.mcds_interval.disabled = True
+            
+        self.toggle_mcds.observe(toggle_mcds_cb)
+       
+        svg_mat_output_row = HBox([Label('Plots:'),self.toggle_svg, HBox([self.svg_interval,Label('min')]), 
+            self.toggle_mcds, HBox([self.mcds_interval,Label('min')])  ])
+
+        # to sync, do this
+        # svg_mat_output_row = HBox( [Label('Plots:'), self.svg_interval, Label('min')]) 
+
+        #write_config_row = HBox([write_config_button, write_config_file])
+        #run_sim_row = HBox([run_button, run_command_str, kill_button])
+        # run_sim_row = HBox([run_button, run_command_str])
+        # run_sim_row = HBox([run_button.w])  # need ".w" for the custom RunCommand widget
+
+        label_blankline = Label('')
+        # toggle_2D_seed_row = HBox([toggle_prng, prng_seed])  # toggle2D
+
+
+        box_layout = Layout(border='1px solid')
+#        domain_box = VBox([label_domain,x_row,y_row,z_row], layout=box_layout)
+        domain_box = VBox([label_domain,x_row,y_row], layout=box_layout)
+        self.tab = VBox([domain_box,
+#                         label_blankline, 
+                         HBox([self.tmax, Label('min')]), self.omp_threads,  
+                         svg_mat_output_row,
+#                         HBox([self.substrate[3], self.diffusion_coef[3], self.decay_rate[3] ]),
+                         ])  # output_dir, toggle_2D_seed_
+#                         ], layout=tab_layout)  # output_dir, toggle_2D_seed_
+
+    # Populate the GUI widgets with values from the XML
+    def fill_gui(self, xml_root):
+        self.xmin.value = float(xml_root.find(".//x_min").text)
+        self.xmax.value = float(xml_root.find(".//x_max").text)
+        self.xdelta.value = float(xml_root.find(".//dx").text)
+    
+        self.ymin.value = float(xml_root.find(".//y_min").text)
+        self.ymax.value = float(xml_root.find(".//y_max").text)
+        self.ydelta.value = float(xml_root.find(".//dy").text)
+    
+        self.zmin.value = float(xml_root.find(".//z_min").text)
+        self.zmax.value = float(xml_root.find(".//z_max").text)
+        self.zdelta.value = float(xml_root.find(".//dz").text)
+        
+        self.tmax.value = float(xml_root.find(".//max_time").text)
+        
+        self.omp_threads.value = int(xml_root.find(".//omp_num_threads").text)
+        
+        if xml_root.find(".//full_data//enable").text.lower() == 'true':
+            self.toggle_mcds.value = True
+        else:
+            self.toggle_mcds.value = False
+        self.mcds_interval.value = int(xml_root.find(".//full_data//interval").text)
+
+        # NOTE: do this *after* filling the mcds_interval, directly above, due to the callback/constraints on them
+        if xml_root.find(".//SVG//enable").text.lower() == 'true':
+            self.toggle_svg.value = True
+        else:
+            self.toggle_svg.value = False
+        self.svg_interval.value = int(xml_root.find(".//SVG//interval").text)
+
+
+    # Read values from the GUI widgets and generate/write a new XML
+    def fill_xml(self, xml_root):
+        # print('config.py fill_xml() !!!!!')
+        # TODO: verify template .xml file exists!
+
+        # TODO: verify valid type (numeric) and range?
+        xml_root.find(".//x_min").text = str(self.xmin.value)
+        xml_root.find(".//x_max").text = str(self.xmax.value)
+        xml_root.find(".//dx").text = str(self.xdelta.value)
+        xml_root.find(".//y_min").text = str(self.ymin.value)
+        xml_root.find(".//y_max").text = str(self.ymax.value)
+        xml_root.find(".//dy").text = str(self.ydelta.value)
+        xml_root.find(".//z_min").text = str(self.zmin.value)
+        xml_root.find(".//z_max").text = str(self.zmax.value)
+        xml_root.find(".//dz").text = str(self.zdelta.value)
+
+        xml_root.find(".//max_time").text = str(self.tmax.value)
+
+        xml_root.find(".//omp_num_threads").text = str(self.omp_threads.value)
+
+        xml_root.find(".//SVG").find(".//enable").text = str(self.toggle_svg.value)
+        xml_root.find(".//SVG").find(".//interval").text = str(self.svg_interval.value)
+        xml_root.find(".//full_data").find(".//enable").text = str(self.toggle_mcds.value)
+        xml_root.find(".//full_data").find(".//interval").text = str(self.mcds_interval.value)
+
+        #    user_details = ET.SubElement(root, "user_details")
+        #    ET.SubElement(user_details, "PhysiCell_settings", name="version").text = "devel-version"
+        #    ET.SubElement(user_details, "domain")
+        #    ET.SubElement(user_details, "xmin").text = "-100"
+
+        #    tree = ET.ElementTree(root)
+        #    tree.write(write_config_file.value)
+        #    tree.write("test.xml")
+
+        # TODO: verify can write to this filename
+#        tree.write(write_config_file.value)
+
+    def get_num_svg_frames(self):
+        if (self.toggle_svg.value):
+            return int(self.tmax.value/self.svg_interval.value)
+        else:
+            return 0
+
+    def get_num_substrate_frames(self):
+        if (self.toggle_mcds.value):
+            return int(self.tmax.value/self.mcds_interval.value)
+        else:
+            return 0

bin/debug.py

+import ipywidgets as widgets
+
+# Provides a simple output widget to contain debug output.
+# Works in callbacks and threads.
+# Does not mess up other outputs.
+debug_view = widgets.Output(layout={'border': '1px solid black'})

bin/pc4covid19.py

+import ipywidgets as widgets
+import xml.etree.ElementTree as ET  # https://docs.python.org/2/library/xml.etree.elementtree.html
+import os
+import glob
+import shutil
+import math
+import datetime
+import tempfile
+from about import AboutTab
+from config import ConfigTab
+from microenv_params import MicroenvTab
+from user_params import UserTab
+# from svg import SVGTab
+from substrates import SubstrateTab
+# from animate_tab import AnimateTab
+from pathlib import Path
+import platform
+import subprocess
+from debug import debug_view
+
+hublib_flag = True
+if platform.system() != 'Windows':
+    try:
+#        print("Trying to import hublib.ui")
+        from hublib.ui import RunCommand, Submit
+        # from hublib2.ui import RunCommand, Submit
+    except:
+        hublib_flag = False
+else:
+    hublib_flag = False
+
+
+# join_our_list = "(Join/ask questions at https://groups.google.com/forum/#!forum/physicell-users)\n"
+
+
+# create the tabs, but don't display yet
+about_tab = AboutTab()
+config_tab = ConfigTab()
+
+xml_file = os.path.join('data', 'PhysiCell_settings.xml')
+full_xml_filename = os.path.abspath(xml_file)
+
+tree = ET.parse(full_xml_filename)  # this file cannot be overwritten; part of tool distro
+xml_root = tree.getroot()
+microenv_tab = MicroenvTab()
+user_tab = UserTab()
+# svg = SVGTab()
+sub = SubstrateTab()
+# animate_tab = AnimateTab()
+
+nanoHUB_flag = False
+if( 'HOME' in os.environ.keys() ):
+    nanoHUB_flag = "home/nanohub" in os.environ['HOME']
+
+
+# callback when user selects a cached run in the 'Load Config' dropdown widget.
+# HOWEVER, beware if/when this is called after a sim finishes and the Load Config dropdown widget reverts to 'DEFAULT'.
+# In that case, we don't want to recompute substrate.py self.numx, self.numy because we're still displaying plots from previous sim.
+def read_config_cb(_b):
+    # with debug_view:
+    #     print("read_config_cb", read_config.value)
+
+    sub.first_time = True
+
+    if read_config.value is None:  #occurs when a Run just finishes and we update pulldown with the new cache dir??
+        # with debug_view:
+        #     print("NOTE: read_config_cb(): No read_config.value. Returning!")
+        # print("NOTE: read_config_cb(): No read_config.value. Returning!")
+        return
+
+    if os.path.isdir(read_config.value):
+        is_dir = True
+        config_file = os.path.join(read_config.value, 'config.xml')
+        # print("read_config_cb(): is_dir=True; config_file=",config_file)
+    else:
+        is_dir = False
+        config_file = read_config.value
+        # print("read_config_cb(): is_dir=False; --- config_file=",config_file)
+
+    if Path(config_file).is_file():
+        # with debug_view:
+        # print("read_config_cb():  calling fill_gui_params with ",config_file)
+        fill_gui_params(config_file)  #should verify file exists!
+
+        # If cells or substrates toggled off in Config tab, toggle off in Plots tab
+        if config_tab.toggle_svg.value == False:
+            sub.cells_toggle.value = False
+            sub.cells_toggle.disabled = True
+        else:
+            sub.cells_toggle.disabled = False
+
+        if config_tab.toggle_mcds.value == False:
+            sub.substrates_toggle.value = False
+            sub.substrates_toggle.disabled = True
+        else:
+            sub.substrates_toggle.disabled = False
+
+    else:
+        # with debug_view:
+        #     print("read_config_cb: ",config_file, " does not exist.")
+        return
+    
+    # update visualization tabs
+    if is_dir: