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Commit 8250236d authored by Vincent Noël's avatar Vincent Noël
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Updated UI

parent 4a93c8cb
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bin/populations.py
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# substrates Tab
# populations Tab
import os, math
from pathlib import Path
from ipywidgets import Layout, Label, Text, Checkbox, Button, BoundedIntText, HBox, VBox, Box, \
FloatText, Dropdown, interactive
import os
from ipywidgets import HBox, interactive
import matplotlib.pyplot as plt
from matplotlib.colors import BoundaryNorm
from matplotlib.ticker import MaxNLocator
from matplotlib.collections import LineCollection
from matplotlib.patches import Circle, Ellipse, Rectangle
from matplotlib.collections import PatchCollection
import matplotlib.colors as mplc
from collections import deque
import numpy as np
import scipy.io
import xml.etree.ElementTree as ET # https://docs.python.org/2/library/xml.etree.elementtree.html
import xml.etree.ElementTree as ET
import glob
import platform
import zipfile
from debug import debug_view
import warnings
hublib_flag = True
if platform.system() != 'Windows':
try:
# print("Trying to import hublib.ui")
from hublib.ui import Download
except:
hublib_flag = False
else:
hublib_flag = False
#warnings.warn(message, mplDeprecation, stacklevel=1)
warnings.filterwarnings("ignore")
......@@ -39,167 +18,122 @@ class PopulationsTab(object):
def __init__(self):
self.output_dir = '.'
# self.output_dir = 'tmpdir'
self.figsize_width_substrate = 15.0 # allow extra for colormap
self.figsize_height_substrate = 8
self.figsize_width_svg = 12.0
self.figsize_height_svg = 12.0
# self.fig = plt.figure(figsize=(7.2,6)) # this strange figsize results in a ~square contour plot
self.first_time = True
self.modulo = 1
self.use_defaults = True
self.svg_delta_t = 1
self.substrate_delta_t = 1
self.svg_frame = 1
self.substrate_frame = 1
self.customized_output_freq = False
self.therapy_activation_time = 1000000
self.max_svg_frame_pre_therapy = 1000000
self.max_substrate_frame_pre_therapy = 1000000
self.svg_xmin = 0
# Probably don't want to hardwire these if we allow changing the domain size
# self.svg_xrange = 2000
# self.xmin = -1000.
# self.xmax = 1000.
# self.ymin = -1000.
# self.ymax = 1000.
# self.x_range = 2000.
# self.y_range = 2000.
self.show_nucleus = False
self.show_edge = True
# initial value
self.field_index = 4
# self.field_index = self.mcds_field.value + 4
self.skip_cb = False
# define dummy size of mesh (set in the tool's primary module)
self.numx = 0
self.numy = 0
self.title_str = ''
tab_height = '1200px'
tab_height = '500px'
constWidth = '180px'
constWidth2 = '150px'
tab_layout = Layout(width='900px', # border='2px solid black',
height=tab_height, ) #overflow_y='scroll')
max_frames = 0
# self.mcds_plot = interactive(self.plot_substrate, frame=(0, max_frames), continuous_update=False)
# self.i_plot = interactive(self.plot_plots, frame=(0, max_frames), continuous_update=False)
self.pop_plot = interactive(self.plot_celltypes, frame=(0,max_frames), continuous_update=False)
self.max_frames = BoundedIntText(
min=0, max=99999, value=max_frames,
description='Max',
layout=Layout(width='160px'),
# layout=Layout(flex='1 1 auto', width='auto'), #Layout(width='160px'),
)
self.max_frames.observe(self.update_max_frames)
help_label = Label('select slider: drag or left/right arrows')
self.tab = VBox([self.max_frames, self.pop_plot])
# self.tab = VBox([controls_box, self.debug_str, self.i_plot, download_row])
def update_max_frames(self,_b):
self.pop_plot.children[0].max = self.max_frames.value
def update(self, rdir=''):
# with debug_view:
# print("substrates: update rdir=", rdir)
# print("substrates: update rdir=", rdir)
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.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), 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, 'snapshot*.svg')))
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.value = int(last_file[-12:-4]) # assumes naming scheme: "snapshot%08d.svg"
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):
if frame <= 0:
return
self.title_str = ''
# if (self.substrates_toggle.value):
# if (True):
self.pop_counts = {}
self.fig = plt.figure(figsize=(self.figsize_width_substrate, self.figsize_height_substrate))
for i in range(0, frame+1):
for i in range(0, frame):
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.") # No: output00000000_microenvironment0.mat
return
if self.pop_counts is None or self.pop_counts.shape[1] <= i:
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_size = dict(zip(unique, counts))
for key, value in pop_size.items():
if key not in self.pop_counts.keys():
if i == 0:
self.pop_counts[key] = [value]
else:
self.pop_counts[key] = [0]*i + [value]
else:
self.pop_counts[key].append(value)
config_file = "config.xml"
cell_lines = {}
if os.path.isfile(config_file):
try:
tree = ET.parse(config_file)
except:
print("Cannot parse",config_file, "- check it's XML syntax.")
return
fname = "output%08d_cells_physicell.mat" % i
full_fname = os.path.join(self.output_dir, fname)
root = tree.getroot()
uep = root.find('.//cell_definitions') # find unique entry point (uep)
for child in uep.findall('cell_definition'):
cell_lines[int(child.attrib["ID"])] = child.attrib["name"]
# print(child.attrib['name'])
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)
ax = self.fig.add_subplot(111)
t_data = []
t_names = []
for t_id, name in cell_lines.items():
if t_id in self.pop_counts.keys():
t_data.append(self.pop_counts[t_id])
t_names.append(name)
# t_data = [value for value in self.pop_counts.values()]
ax.stackplot(range(0, frame), t_data , labels=t_names)
ax.legend(labels=t_names, loc='upper center', bbox_to_anchor=(0.5, -0.05), ncol=2)
ax.margins(0, 0) # Set margins to avoid "whitespace"
for t_id, name in self.cell_lines.items():
if self.pop_counts[t_id, :].any():
t_data.append(self.pop_counts[t_id, :])
t_names.append(name)
# if name not in self.palette.keys():
# self.palette.update({name: "C%d" % (len(self.palette.keys()) % 10)})
# color_list = [self.palette[t_name] for t_name in t_names]
t_times = np.array(range(0, self.pop_counts.shape[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)
ax.stackplot(
t_times,
t_data,
labels=t_names,
# colors=color_list
)
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)")
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