v3

README.md

-# pc4covid19 - COVID19 tissue simulator nanoHUB app
+# pc4covid19 - COVID19 (SARS-CoV-2) tissue simulator nanoHUB app
 
-**Version:** 2.1 - uses the core model at https://github.com/pc4covid19/COVID19/releases/tag/0.2.1
+**Version:** 3.0
 
-**Release date:** 26 April 2020 
+**Release date:** 3 July 2020 
 
 ## Overview
 This repository contains code and data for the nanoHUB app https://nanohub.org/tools/pc4covid19.
@@ -20,9 +20,12 @@ for a summary of changes to the model.
 
 **This model will be continually refined with input from the community, particularly experts in infectious diseases. The validation state will be updated as this progresses.**
 
-## Release summary:
-### 2.1:
-Sync up with the version number of the published app, https://nanohub.org/tools/pc4covid19, and include a reference to the version of the core model in this README.
+## Release summary: 
+### 3.0:
+The major change to the GUI in this release is the addition of a 'Cell Types' tab.
+This allows editing parameters associated with `<cell_definitions>` in the configuration file.
+
+This version also includes a `<style>` block in the Jupyter notebook that fixed an unwanted scrollbar in the lengthy `About` tab.
 
 ### 2.0:
 The major change to the GUI in this release is the addition of an 'Animate' tab.

bin/about.py

-from ipywidgets import Output
+from ipywidgets import Output, Tab, Layout
 from IPython.display import display, HTML
 
 class AboutTab(object):
 
     def __init__(self):
-        # self.tab = Output(layout={'height': '600px'})
+        # self.tab = Output(layout={'height': '900px'})
+        # self.tab = Output(layout={height=’85%’,min_height=’350px’})
+        # self.background = Output(layout={'height': 'auto'})
+        # self.legend = Output(layout={'height': 'auto'})
         self.tab = Output(layout={'height': 'auto'})
+
+        # self.tab.append_display_data(HTML(filename='doc/about-good.html'))
+        # self.tab.append_display_data(HTML(filename='doc/about-bad.html'))
+        # self.background.append_display_data(HTML(filename='doc/about_background.html'))
+        # self.legend.append_display_data(HTML(filename='doc/about_legend.html'))
         self.tab.append_display_data(HTML(filename='doc/about.html'))
         
+        # tab_layout = Layout(width='auto',height='auto', overflow_y='scroll',)   # border='2px solid black',
+        # titles = ['Background', 'Legend']
+        # self.tab = Tab(children=[self.background, self.legend],
+        #            _titles={i: t for i, t in enumerate(titles)},
+        #            layout=tab_layout)

bin/pc4covid19.py

@@ -10,6 +10,11 @@ from about import AboutTab
 from config import ConfigTab
 from microenv_params import MicroenvTab
 from user_params import UserTab
+try:
+    from cell_types import CellTypesTab
+except:
+    # print("cell_types.py does not exist due to no <cell_definitions>")
+    pass
 # from svg import SVGTab
 from substrates import SubstrateTab
 from animate_tab import AnimateTab
@@ -42,8 +47,13 @@ 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()
+
+if xml_root.find('.//cell_definitions'):
+    cell_types_tab = CellTypesTab()
+
 # svg = SVGTab()
 sub = SubstrateTab()
 animate_tab = AnimateTab()
@@ -132,12 +142,12 @@ def write_config_file(name):
     sub.update_params(config_tab, user_tab)
     # sub.numx =  math.ceil( (config_tab.xmax.value - config_tab.xmin.value) / config_tab.xdelta.value )
     # sub.numy =  math.ceil( (config_tab.ymax.value - config_tab.ymin.value) / config_tab.ydelta.value )
-    # print("pc4covid19.py: ------- sub.numx, sub.numy = ", sub.numx, sub.numy)
+    # print("pc4covid19_v3.py: ------- sub.numx, sub.numy = ", sub.numx, sub.numy)
 
 
 # callback from write_config_button
 # def write_config_file_cb(b):
-#     path_to_share = os.path.join('~', '.local','share','pc4covid19')
+#     path_to_share = os.path.join('~', '.local','share','pc4covid19_v3')
 #     dirname = os.path.expanduser(path_to_share)
 
 #     val = write_config_box.value
@@ -151,7 +161,7 @@ def write_config_file(name):
 # default & previous config options)
 def get_config_files():
     cf = {'DEFAULT': full_xml_filename}
-    path_to_share = os.path.join('~', '.local','share','pc4covid19')
+    path_to_share = os.path.join('~', '.local','share','pc4covid19_v3')
     dirname = os.path.expanduser(path_to_share)
     try:
         os.makedirs(dirname)
@@ -163,12 +173,12 @@ def get_config_files():
 
     # Find the dir path (full_path) to the cached dirs
     if nanoHUB_flag:
-        full_path = os.path.expanduser("~/data/results/.submit_cache/pc4covid19")  # does Windows like this?
+        full_path = os.path.expanduser("~/data/results/.submit_cache/pc4covid19_v3")  # does Windows like this?
     else:
         # local cache
         try:
             cachedir = os.environ['CACHEDIR']
-            full_path = os.path.join(cachedir, "pc4covid19")
+            full_path = os.path.join(cachedir, "pc4covid19_v3")
         except:
             # print("Exception in get_config_files")
             return cf
@@ -215,7 +225,7 @@ def run_done_func(s, rdir):
     
     if nanoHUB_flag:
         # Email the user that their job has completed
-        os.system("submit  mail2self -s 'nanoHUB pc4covid19' -t 'Your Run completed.'&")
+        os.system("submit  mail2self -s 'nanoHUB pc4covid19_v3' -t 'Your Run completed.'&")
 
     # save the config file to the cache directory
     shutil.copy('config.xml', rdir)
@@ -238,7 +248,6 @@ def run_done_func(s, rdir):
 
     animate_tab.gen_button.disabled = False
 
-
     # with debug_view:
     #     print('RDF DONE')
 
@@ -290,7 +299,7 @@ def run_sim_func(s):
 
     if nanoHUB_flag:
         if remote_cb.value:
-            s.run(run_name, "-v ncn-hub_M@brown -n 8 -w 1440 pc4covid19-r7 config.xml")   # "-r7" suffix??
+            s.run(run_name, "-v ncn-hub_M@brown -n 8 -w 1440 pc4covid19_v3-r7 config.xml")   # "-r7" suffix??
         else:
             # read_config.index = 0   # reset Dropdown 'Load Config' to 'DEFAULT' when Run interactively
             s.run(run_name, "--local ../bin/myproj config.xml")
@@ -304,7 +313,6 @@ def run_sim_func(s):
     #     print('run_sim_func DONE')
 
 
-# callback for stdout from simulation
 def outcb(s):
     # This is called when new output is received.
     # Only update file list for certain messages: 
@@ -314,7 +322,7 @@ def outcb(s):
         # svg.update('')
         # sub.update('')
         # sub.update_params(config_tab)
-        sub.update()  # this only updates the "# cell frames" (max_frames) when stdout = "current simulated time"
+        sub.update()
     return s
 
 
@@ -357,14 +365,14 @@ if nanoHUB_flag:
     run_button = Submit(label='Run',
                        start_func=run_sim_func,
                         done_func=run_done_func,
-                        cachename='pc4covid19',
+                        cachename='pc4covid19_v3',
                         showcache=False,
                         outcb=outcb)
 else:
     if (hublib_flag):
         run_button = RunCommand(start_func=run_sim_func,
                             done_func=run_done_func,
-                            cachename='pc4covid19',
+                            cachename='pc4covid19_v3',
                             showcache=False,
                             outcb=outcb)  
     else:
@@ -386,18 +394,24 @@ if nanoHUB_flag or hublib_flag:
     read_config.observe(read_config_cb, names='value') 
 
 tab_height = 'auto'
-tab_layout = widgets.Layout(width='auto',height=tab_height, overflow_y='scroll',)   # border='2px solid black',
-titles = ['About', 'Config Basics', 'Microenvironment', 'User Params', 'Out: Plots', 'Animate']
-# titles = ['About', 'Config Basics', 'Microenvironment', 'User Params', 'Out: Plots']
-
-# tabs = widgets.Tab(children=[about_tab.tab, config_tab.tab, microenv_tab.tab, user_tab.tab, sub.tab],
-tabs = widgets.Tab(children=[about_tab.tab, config_tab.tab, microenv_tab.tab, user_tab.tab, sub.tab, animate_tab.tab],
+#tab_layout = widgets.Layout(width='auto',height=tab_height, overflow_y='scroll',)   # border='2px solid black',
+tab_layout = widgets.Layout(width='auto',height=tab_height)   # border='2px solid black',
+
+if xml_root.find('.//cell_definitions'):
+    titles = ['About', 'Config Basics', 'Microenvironment', 'User Params', 'Cell Types', 'Out: Plots', 'Animate']
+    tabs = widgets.Tab(children=[about_tab.tab, config_tab.tab, microenv_tab.tab, user_tab.tab, cell_types_tab.tab, sub.tab, animate_tab.tab],
+                   _titles={i: t for i, t in enumerate(titles)})
+#                   layout=tab_layout)
+else:
+    titles = ['About', 'Config Basics', 'Microenvironment', 'User Params', 'Out: Plots', 'Animate']
+    tabs = widgets.Tab(children=[about_tab.tab, config_tab.tab, microenv_tab.tab, user_tab.tab, sub.tab, animate_tab.tab],
                    _titles={i: t for i, t in enumerate(titles)},
                    layout=tab_layout)
 
 homedir = os.getcwd()
 
-tool_title = widgets.Label(r'\(\textbf{PhysiCell model of COVID19}\)')
+# tool_title = widgets.Label(r'\(\textbf{pc4covid19_v3}\)')
+tool_title = widgets.Label(r'\(\textbf{PhysiCell model for SARS-CoV-2}\)')
 if nanoHUB_flag or hublib_flag:
     # define this, but don't use (yet)
     remote_cb = widgets.Checkbox(indent=False, value=False, description='Submit as Batch Job to Clusters/Grid')

bin/substrates.py

@@ -75,6 +75,7 @@ class SubstrateTab(object):
         # self.y_range = 2000.
 
         self.show_nucleus = False
+        self.semi_transparent = False
         self.show_edge = True
 
         substrates_default_disabled_flag = True  # True = disable them by default; False=enable them
@@ -95,8 +96,8 @@ class SubstrateTab(object):
         tab_height = '500px'
         constWidth = '180px'
         constWidth2 = '150px'
-        tab_layout = Layout(width='900px',   # border='2px solid black',
-                            height=tab_height, ) #overflow_y='scroll')
+        # tab_layout = Layout(width='900px',   # border='2px solid black',
+                            # height=tab_height, ) #overflow_y='scroll')
 
         max_frames = 1   
         # self.mcds_plot = interactive(self.plot_substrate, frame=(0, max_frames), continuous_update=False)  
@@ -262,13 +263,30 @@ class SubstrateTab(object):
         def cell_nucleus_toggle_cb(b):
             # self.update()
             if (self.cell_nucleus_toggle.value):  
-                self.show_nucleus = True
+                # self.show_nucleus = True
+                self.show_nucleus = False
             else:
                 self.show_nucleus = False
             self.i_plot.update()
 
         self.cell_nucleus_toggle.observe(cell_nucleus_toggle_cb)
 
+        #---------------------
+        self.cell_semitrans_toggle = Checkbox(
+            description='translucent',
+            disabled=False,
+            value = self.semi_transparent,
+#           layout=Layout(width=constWidth2),
+        )
+        def cell_semitrans_toggle_cb(b):
+            if (self.cell_semitrans_toggle.value):  
+                self.semi_transparent = True
+            else:
+                self.semi_transparent = False
+            self.i_plot.update()
+
+        self.cell_semitrans_toggle.observe(cell_semitrans_toggle_cb)
+
         #----
         self.cell_edges_toggle = Checkbox(
             description='edges',
@@ -298,9 +316,12 @@ class SubstrateTab(object):
             if (self.cells_toggle.value):
                 self.cell_edges_toggle.disabled = False
                 self.cell_nucleus_toggle.disabled = False
+                self.cell_semitrans_toggle.disabled = False
+                # self.semi_transparent = True
             else:
                 self.cell_edges_toggle.disabled = True
                 self.cell_nucleus_toggle.disabled = True
+                self.cell_semitrans_toggle.disabled = True
 
         self.cells_toggle.observe(cells_toggle_cb)
 
@@ -355,7 +376,9 @@ class SubstrateTab(object):
                             align_items='stretch',
                             flex_direction='row',
                             display='flex')) 
-        row1b = Box( [self.cells_toggle, self.cell_nucleus_toggle, self.cell_edges_toggle], layout=Layout(border='1px solid black',
+        # row1b = Box( [self.cells_toggle, self.cell_nucleus_toggle, self.cell_edges_toggle], layout=Layout(border='1px solid black',
+        # row1b = Box( [self.cells_toggle, self.cell_semitrans_toggle, self.cell_edges_toggle], layout=Layout(border='1px solid black',
+        row1b = Box( [self.cells_toggle, self.cell_edges_toggle], layout=Layout(border='1px solid black',
                             width='50%',
                             height='',
                             align_items='stretch',
@@ -862,17 +885,19 @@ class SubstrateTab(object):
         # print('max=',markers_size.max())
 
         #rwh - temp fix - Ah, error only occurs when "edges" is toggled on
+        # alpha_val = 1.0
+        # if (self.semi_transparent):
+        #     alpha_val = 0.5
         if (self.show_edge):
             try:
-                # plt.scatter(xvals,yvals, s=markers_size, c=rgbs, edgecolor='black', linewidth=0.5)
-                self.circles(xvals,yvals, s=rvals, color=rgbs, edgecolor='black', linewidth=0.5)
-                # cell_circles = self.circles(xvals,yvals, s=rvals, color=rgbs, edgecolor='black', linewidth=0.5)
+                # self.circles(xvals,yvals, s=rvals, color=rgbs, edgecolor='black', linewidth=0.5, alpha=alpha_val)
+                cell_circles = self.circles(xvals,yvals, s=rvals, color=rgbs, edgecolor='black', linewidth=0.5)
                 # plt.sci(cell_circles)
             except (ValueError):
                 pass
         else:
-            # plt.scatter(xvals,yvals, s=markers_size, c=rgbs)
             self.circles(xvals,yvals, s=rvals, color=rgbs)
+            # self.circles(xvals,yvals, s=rvals, color=rgbs, alpha=alpha_val, edgecolor=None )
 
         # if (self.show_tracks):
         #     for key in self.trackd.keys():