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Commit 2636e701 authored by Randy Heiland's avatar Randy Heiland
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cleanup

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tmpdir/bin/about-rwh.py deleted 100644 → 0
View file @ 2aa35629
from ipywidgets import Output
from IPython.display import display, HTML
class AboutTab(object):
def __init__(self):
# self.tab = Output(layout={'height': '900px'})
# self.tab = Output(layout={height=’85%’,min_height=’350px’})
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.tab.append_display_data(HTML(filename='doc/about_with_img.html'))
self.tab.append_display_data(HTML(filename='doc/about-yafei2.html'))
tmpdir/bin/about.py deleted 100644 → 0
View file @ 2aa35629
from ipywidgets import Output, Tab, Layout
from IPython.display import display, HTML
class AboutTab(object):
def __init__(self):
# 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)
tmpdir/bin/about_2tabs.py deleted 100644 → 0
View file @ 2aa35629
from ipywidgets import Output, Tab, Layout
from IPython.display import display, HTML
class AboutTab(object):
def __init__(self):
# 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.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'))
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)
tmpdir/bin/animate_tab.py deleted 100644 → 0
View file @ 2aa35629
from ipywidgets import Button, Label, BoundedIntText, HBox, VBox, Output, HTML, Layout
from IPython.display import display
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from PIL import Image
import os
import glob
import subprocess
import time
import platform
import zipfile
import shutil
from pathlib import Path
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
# hublib_flag = False # shared testing
class AnimateTab(object):
def __init__(self):
self.mp4_zip_file = "cells_mp4.zip"
self.mp4_file = "cells.mp4"
self.instructions = Label("After a simulation completes, generate a video of cells (from SVG files). Does not work for cached results yet.")
self.feedback = Label(" ")
# self.feedback.value = "Converting all svg to jpg..."
self.gen_button = Button(
description='Generate video',
button_style='success', # 'success', 'info', 'warning', 'danger' or ''
tooltip='Generate a MP4 video of cells',
)
self.gen_button.disabled = True
self.gen_button.on_click(self.gen_button_cb)
fps_style = {'description_width': '35%'}
fps_layout = {'width': '85px'}
# tooltip='frames per sec', -- tooltip not available for *Text !
self.fps = BoundedIntText(description="fps=", value=5, min=1, max=30, step=1,
style=fps_style, layout=fps_layout)
size_style = {'description_width': '50%'}
size_layout = {'width': '150px'}
self.size = BoundedIntText(description="w,h(pixels)=", value=500, min=250, max=1500, step=10, disabled=False, tooltip='width, height of video',
style=size_style, layout=size_layout)
self.video = HTML( value="",
placeholder='',
description='',
layout= Layout(visibility='hidden')
)
if (hublib_flag):
self.download_mp4_button = Download(self.mp4_zip_file, style='success', icon='cloud-download',
tooltip='Download mp4 (you need to allow pop-ups in your browser)')
self.download_mp4_button.w.disabled = True
self.tab = VBox([self.instructions, HBox([ self.gen_button, self.fps, self.size, self.feedback,
self.download_mp4_button.w]), self.video])
else:
self.tab = VBox([self.instructions, HBox([self.gen_button, self.fps, self.size, self.feedback]), self.video])
#---------------------------
# callback for the 'Generate video' button
def gen_button_cb(self, b):
self.gen_button.description = 'working'
self.gen_button.button_style = 'warning' # 'success','info','warning','danger' or ''
self.gen_button.disabled = True
self.fps.disabled = True
self.size.disabled = True
feedback_base = "Converting all svg to jpg..."
self.feedback.value = feedback_base
cwd = os.getcwd()
if not 'tmpdir' in cwd:
tdir = os.path.abspath('tmpdir')
os.chdir(tdir)
num_svg = len(glob.glob('snap*.svg'))
idx_start = 0
idx_end = num_svg
for idx in range(idx_start,idx_end): # perhaps allow stepsize > 1
fname = "snapshot%08d" % idx
svg_file = fname + ".svg"
jpg_file = fname + ".jpg"
subprocess.Popen(["convert", svg_file, jpg_file])
delay = 2 # secs
for idx in range(num_svg):
num_jpg = len(glob.glob('snap*.jpg'))
self.feedback.value = feedback_base + str(num_jpg) + " of " + str(num_svg)
time.sleep(delay)
if num_jpg == num_svg:
break
img_width = self.size.value
if (img_width % 2): # req divisible by 2
img_width += 1
img_height = img_width + 36
try:
os.remove(self.mp4_file)
except OSError:
pass
cmd = 'ffmpeg -framerate ' + str(self.fps.value) + ' -i snapshot%08d.jpg -vf scale=' + str(img_width) + ':' + str(img_height) + ' ' + self.mp4_file
self.feedback.value = "Converting all jpg to mp4..."
os.system(cmd)
self.gen_button.description = 'Generate'
self.gen_button.button_style = 'success'
self.gen_button.disabled = False
self.fps.disabled = False
self.size.disabled = False
zipfile.ZipFile(self.mp4_zip_file, mode='w').write(self.mp4_file)
try:
os.remove(os.path.join('..', self.mp4_zip_file))
except OSError:
pass
shutil.move(self.mp4_zip_file, "..")
self.download_mp4_button.w.disabled = False
self.feedback.value = "Done. (Wait for animation to appear below)"
# Generate/display the animation of jpgs
plt.ioff()
self.fig = plt.figure(figsize= [13, 13])
# print("------ gen_button_cb")
self.anim_imgs = []
fname = self.mp4_file
# for idx in range(0,19,3):
success = True
for idx in range(num_jpg):
fname = 'snapshot%08d.jpg' % idx
# fname = 'img%08d.jpg' % idx
# print(fname)
try:
img = Image.open(fname)
except:
self.feedback.value = "Error: cannot open " + fname
success = False
break
img.thumbnail((700, 700), Image.ANTIALIAS)
im = plt.imshow(img, animated=True)
self.anim_imgs.append([im])
if success:
self.mpl_anim = animation.ArtistAnimation(self.fig, self.anim_imgs, interval=500, blit=True, repeat_delay=1000)
self.video.value = self.mpl_anim.to_html5_video()
self.video.layout.visibility = None
self.feedback.value = "Done."
plt.close(self.fig)
tmpdir/bin/cell_types-keep.py deleted 100644 → 0
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tmpdir/bin/cell_types.py deleted 100644 → 0
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tmpdir/bin/config.py deleted 100644 → 0
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# 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
tmpdir/bin/debug.py deleted 100644 → 0
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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'})
tmpdir/bin/microenv_params.py deleted 100644 → 0
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tmpdir/bin/pc4covid19.py deleted 100644 → 0
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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
try:
from cell_types import CellTypesTab
except: