Skip to content

Added population size tab #10

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
vincent-noel wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Added population size tab #10

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
154 changes: 154 additions & 0 deletions bin/populations.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,154 @@
# populations Tab

import os

from ipywidgets import HBox, interactive
import matplotlib.pyplot as plt
from matplotlib import rcParams
import numpy as np
import scipy.io
import xml.etree.ElementTree as ET
import glob
import warnings

#warnings.warn(message, mplDeprecation, stacklevel=1)
warnings.filterwarnings("ignore")

class PopulationsTab(object):

def __init__(self):

self.output_dir = '.'

self.figsize_width = 15.0
self.figsize_height = 8

config_file = "data/PhysiCell_settings.xml"

self.cell_lines = {}
self.full_data_interval = 0
self.full_data_units = "min"
self.pop_counts = None
self.list_colors = rcParams["axes.prop_cycle"].by_key()["color"]
self.palette = {}

if os.path.isfile(config_file):

try:
tree = ET.parse(config_file)
except:
print("Cannot parse", config_file, "- check it's XML syntax.")
return

root = tree.getroot()
uep = root.find('.//cell_definitions') # find unique entry point (uep)
for child in uep.findall('cell_definition'):
self.cell_lines[int(child.attrib["ID"])] = child.attrib["name"]

uep = root.find('.//save/full_data/interval')
raw_interval = uep.text
units = uep.attrib['units']
if units == "min":
self.full_data_interval = int(raw_interval)
elif units == "hour":
self.full_data_interval = int(raw_interval)*60

self.max_frames = 0
self.pop_plot = interactive(self.plot_celltypes, frame=(0, self.max_frames), stacked=True, continuous_update=False)

self.tab = HBox([self.pop_plot])

def update(self, rdir=''):
if rdir:
self.output_dir = rdir

all_files = sorted(glob.glob(os.path.join(self.output_dir, 'output*_cells_physicell.mat')))
if len(all_files) > 0:
last_file = all_files[-1]
self.max_frames = int(last_file[-28:-20]) # assumes naming scheme: "output%08d_cells_physicell.mat"
self.pop_plot.children[0].max = self.max_frames

def plot_celltypes(self, frame=None, stacked=True):

if frame <= 0:
return

for i in range(0, frame+1):

if self.pop_counts is None or self.pop_counts.shape[1] <= i:

fname = "output%08d_cells_physicell.mat" % i
full_fname = os.path.join(self.output_dir, fname)

if not os.path.isfile(full_fname):
print("Once output files are generated, click the slider.")
return

info_dict = {}
scipy.io.loadmat(full_fname, info_dict)

M = info_dict['cells'][5, :].astype(int)

unique, counts = np.unique(M, return_counts=True)

pop_count = np.zeros((len(self.cell_lines), 1))
pop_count[unique, 0] = counts

if i == 0:
self.pop_counts = pop_count

else:
self.pop_counts = np.append(self.pop_counts, pop_count, axis=1)

t_data = []
y_max = 0
t_names = []

for t_id, name in self.cell_lines.items():
if self.pop_counts[t_id, 0:frame+1].any():
y_max = max(y_max, np.max(self.pop_counts[t_id, 0:frame+1]))
t_data.append(self.pop_counts[t_id, 0:frame+1])
t_names.append(name)
if name not in self.palette.keys():
self.palette.update({name: self.list_colors[len(self.palette.keys()) % 10]})

color_list = [self.palette[t_name] for t_name in t_names]

t_times = np.array(range(0, frame+1))
t_times = t_times * self.full_data_interval
t_unit = self.full_data_units

if np.max(t_times) > 1000:
if t_unit == "min":
t_times = t_times / 60
t_unit = "hour"

elif t_unit == "hour":
t_times = t_times / 24
t_unit = "day"

fig = plt.figure(figsize=(self.figsize_width, self.figsize_height))
ax = fig.add_subplot(111)

if stacked:
ax.stackplot(
t_times,
t_data,
labels=t_names,
colors=color_list
)
else:
for t_datum, t_label in zip(t_data, t_names):
ax.plot(
t_times,
t_datum,
label=t_label,
color=self.palette[t_label]

)
ax.set_ylim(0, y_max*1.1)

ax.legend(labels=t_names, loc='upper center', bbox_to_anchor=(0.5, -0.1), ncol=4)
ax.margins(0, 0) # Set margins to avoid "whitespace"
ax.set_xlabel("Time (" + t_unit + "s)")
ax.set_ylabel("Population size (cells)")
15 changes: 11 additions & 4 deletions bin/tool4nanobio.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
pass
# from svg import SVGTab
from substrates import SubstrateTab
from populations import PopulationsTab
from animate_tab import AnimateTab
from pathlib import Path
import platform
Expand Down Expand Up @@ -56,6 +57,7 @@

# svg = SVGTab()
sub = SubstrateTab()
populations = PopulationsTab()
animate_tab = AnimateTab()

nanoHUB_flag = False
Expand Down Expand Up @@ -116,6 +118,7 @@ def read_config_cb(_b):
# print("read_config_cb(): is_dir True, calling update_params")
sub.update_params(config_tab, user_tab)
sub.update(read_config.value)
populations.update(read_config.value)
# else: # may want to distinguish "DEFAULT" from other saved .xml config files
# FIXME: really need a call to clear the visualizations
# svg.update('')
Expand Down Expand Up @@ -249,6 +252,7 @@ def run_done_func(s, rdir):
# and update visualizations
# svg.update(rdir)
sub.update(rdir)
populations.update(rdir)

animate_tab.gen_button.disabled = False

Expand Down Expand Up @@ -299,6 +303,7 @@ def run_sim_func(s):
# svg.update(tdir)
# sub.update_params(config_tab)
sub.update(tdir)
populations.update(tdir)
# animate_tab.update(tdir)

if nanoHUB_flag:
Expand Down Expand Up @@ -327,6 +332,7 @@ def outcb(s):
# sub.update('')
# sub.update_params(config_tab)
sub.update()
populations.update()
return s


Expand Down Expand Up @@ -360,6 +366,7 @@ def run_button_cb(s):
# svg.update(tdir)
# sub.update_params(config_tab)
sub.update(tdir)
physiboss.update(tdir)

subprocess.Popen(["../bin/myproj", "config.xml"])

Expand Down Expand Up @@ -401,13 +408,13 @@ def run_button_cb(s):
tab_layout = widgets.Layout(width='auto',height=tab_height, overflow_y='scroll',) # 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 = ['About', 'Config Basics', 'Microenvironment', 'User Params', 'Cell Types', 'Out: Plots', 'Out: Populations', 'Animate']
tabs = widgets.Tab(children=[about_tab.tab, config_tab.tab, microenv_tab.tab, user_tab.tab, cell_types_tab.tab, sub.tab, populations.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 = ['About', 'Config Basics', 'Microenvironment', 'User Params', 'Out: Plots', 'Out: Populations', 'Animate']
tabs = widgets.Tab(children=[about_tab.tab, config_tab.tab, microenv_tab.tab, user_tab.tab, sub.tab, populations.tab, animate_tab.tab],
_titles={i: t for i, t in enumerate(titles)},
layout=tab_layout)

Expand Down