def reDraw(self):
self.delete("all")
self.create_rectangle(self.border,
self.border,
GAME_SIZE - self.border,
GAME_SIZE - self.border,
fill='misty rose',
outline='misty rose')
if self.victory:
self['bg'] = 'pale green'
else:
self['bg'] = 'gray90'
for key, stick in self.sticks.items():
val = stick[2]
stick_col_rgb = utils.shift_hue(BASE_COL, BASE_DELTA * (val - 1))
stick_col_hex = utils.rgb_to_hex(stick_col_rgb)
if key in self.collided:
col = 'black'
elif self._tag == key:
stick_col_rgb = utils.scale_brightness(stick_col_rgb,
BASE_SCALE)
col = utils.rgb_to_hex(stick_col_rgb)
else:
col = stick_col_hex
self.drawStick(stick, key, col=col)
def plot_line(self, line):
"""
Decides, for each line, how we're going to plot, normal or with intensities
"""
if line.plot_line:
if not WorldState.Instance().session_dict['normalised']:
if not line.intense_plot:
self.axes.plot(line.original_time,
line.original_results,
label=line.species,
color=rgb_to_hex(line.rgb_tuple),
alpha=1,
lw=line.thickness)
else:
for (sub_plot, new_colour) in line.sub_plot_tuples:
self.axes.plot(line.interpolated_time,
sub_plot,
color=new_colour,
lw=line.thickness)
else:
if not line.intense_plot:
self.axes.plot(line.original_time,
line.normalised_results,
label=line.species,
color=rgb_to_hex(line.rgb_tuple),
alpha=1,
lw=line.thickness)
else:
for (sub_plot, new_colour) in line.normalised_sub_plots:
self.axes.plot(line.interpolated_time,
sub_plot,
color=new_colour,
lw=line.thickness)
def by_hex(color_name) -> 'html':
# extract RGB
r, g, b = utils.hex_to_rgb(color_name)
#
msg = 'Color: #{}; RGB({}, {}, {}); '.format(color_name, r, g, b)
# make a sorted array
cp_colors = copy.copy(tikkurila_colors.COLORS)
for clr in cp_colors:
clr[4] = abs(clr[0] - r) + abs(clr[1] - g) + abs(clr[2] - b)
# sort
from operator import itemgetter
cp_colors.sort(key=itemgetter(4))
# hsl
h, l, s = colorsys.rgb_to_hls(r, g, b)
msg += 'HLS: {0:.3f}, {1:.3f}, {2:.3f}.'.format(h, l, s)
# result
return render_template(
'color_by_hex.html',
the_title=TITLE,
the_note='',
the_result='',
the_name_color0=msg,
the_color0=utils.rgb_to_hex(r, g, b),
the_color1=utils.rgb_to_hex(cp_colors[0][0], cp_colors[0][1],
cp_colors[0][2]),
the_color2=utils.rgb_to_hex(cp_colors[1][0], cp_colors[1][1],
cp_colors[1][2]),
the_color3=utils.rgb_to_hex(cp_colors[2][0], cp_colors[2][1],
cp_colors[2][2]),
the_name_color1=cp_colors[0][3],
the_name_color2=cp_colors[1][3],
the_name_color3=cp_colors[2][3],
)
def __init__(self, results, time, csv, key, colour, graph_width,
graph_height, xmin, xmax, ymin, ymax):
self.results = results
self.original_results = results
self.interpolated_results = []
self.normalised_results = []
self.original_time = time
self.interpolated_time = []
self.horizontal_scale = float(xmax - xmin) / graph_width
self.vertical_scale = float(ymax - ymin) / graph_height
self.length = self.calc_line_length(self.results, time)
self.guide_points = 1000
self.min = 0
self.max = 0
self.species = key
self.plot_line = True
self.intense_plot = False
self.interpolated_results, self.interpolated_time = self.interpolate(
self.results, time)
self.interval = len(self.interpolated_results) / 100
self.rgb_tuple = colour
self.flat_colour = rgb_to_hex(colour)
self.thickness = 2
self.colour_change_points = []
self.seg_colour = None
self.sub_plot_tuples = self.plot_sub_plots(self.interpolated_results,
self.interval)
self.past_points = []
self.counter = 0
self.normalised_sub_plots = []
self.normalise()
self.sub_lists = self.slice_lists(self.interpolated_results)
self.debug_name = "Begin"
def __init__(self, results, time, csv, key, colour, graph_width, graph_height, xmin, xmax, ymin, ymax):
self.results = results
self.original_results = results
self.interpolated_results = []
self.normalised_results = []
self.original_time = time
self.interpolated_time = []
self.horizontal_scale = float(xmax - xmin) / graph_width
self.vertical_scale = float(ymax - ymin) / graph_height
self.length = self.calc_line_length(self.results, time)
self.guide_points = 1000
self.min = 0
self.max = 0
self.species = key
self.plot_line = True
self.intense_plot = False
self.interpolated_results, self.interpolated_time = self.interpolate(self.results, time)
self.interval = len(self.interpolated_results)/100
self.rgb_tuple = colour
self.flat_colour = rgb_to_hex(colour)
self.thickness = 2
self.colour_change_points = []
self.seg_colour = None
self.sub_plot_tuples = self.plot_sub_plots(self.interpolated_results, self.interval)
self.past_points = []
self.counter = 0
self.normalised_sub_plots = []
self.normalise()
self.sub_lists = self.slice_lists(self.interpolated_results)
self.debug_name = "Begin"
def plot_sub_plots(self, results, interval, debug=False):
"""
Plots the sub plots and works out what colour the line should be
this is for colour intensity plot
"""
sub_plots = self.build_colour_plot_arrays(results, interval)
sub_plot_tuples = []
self.colour_change_points = []
for sub_plot in sub_plots:
count = 0
current = 0
while True:
if (sub_plot[count] is not None):
current = sub_plot[count]
break
count += 1
intensity = ((
(current - self.min) / float(1 + self.max - self.min)) *
(_MAX_INTENSITY - _MIN_INTENSITY)) + _MIN_INTENSITY
alpha = intensity / 255
new_colour = rgb_to_hex(rgba_to_rgb(self.rgb_tuple, alpha))
self.colour_change_points.append((count, new_colour))
sub_plot_tuples.append((sub_plot, new_colour))
self.seg_colour = self.colour_change_points[0][1]
return sub_plot_tuples
def choose_background_color(self):
color = colorchooser.askcolor()
if color[1]:
State.background_color = color[1]
State.linenumbering_color = rgb_to_hex(
[int(abs(i - 30)) for i in color[0]])
self.frame_color.body_color_label.config(
text=f'Background color: {State.background_color}')
def draw_stuff(stuff, fill):
outline = outline_color
if not (outline_color_delta is None or fill is None):
outline = gr.offset_color(fill, outline_color_delta)
if not fill is None:
fill = u.rgb_to_hex(*fill)
if not outline is None:
outline = u.rgb_to_hex(*outline)
if isinstance(stuff, gr.Polygon):
canvas.draw_polygon(stuff, fill, outline)
if do_svg:
svg_canvas.draw_polygon(stuff, fill=fill, stroke=outline)
elif isinstance(stuff, gr.Circle):
canvas.draw_circle(stuff, fill, outline)
if do_svg:
svg_canvas.draw_circle(stuff, fill=fill, stroke=outline)
async def role_info(self, ctx: utils.CustomContext, *roles: Role):
"""Get information on a given role."""
embed_list = []
for role in roles:
role_perms = []
permissions_dict = {
"kick_members": "Kick Members",
"ban_members": "Ban Members",
"administrator": "Administrator",
"manage_channels": "Manage Channels",
"manage_guild": "Manage Server",
"manage_messages": "Manage Messages",
"mention_everyone": "Mention Everyone",
"mute_members": "Mute Members (VC)",
"deafen_members": "Deafen Members (VC)",
"move_members": "Move Members (VC)",
"manage_nicknames": "Manage Nicknames",
"manage_roles": "Manage Roles"
}
permissions = dict(role.permissions)
for permission, true_false in permissions.items():
if true_false is True:
if (perm :=
permissions_dict.get(str(permission))) is not None:
role_perms.append(f"✅ {perm}")
repr_permissions = '\n'.join(role_perms)
created_at_str = f"{role.created_at.day}/{role.created_at.month}/{role.created_at.year} {role.created_at.hour}:{role.created_at.minute}:{role.created_at.second}"
role_colour = (role.colour.r, role.colour.g, role.colour.b)
fields = [
["Name", role.name, True],
["Mention", f"`{role.mention}`", True],
["Created At", created_at_str, True],
["Role Position", role.position, True],
["Hoisted", role.hoist, True],
["Mentionable", role.mentionable, True],
["Colour", utils.rgb_to_hex(role_colour), True],
["Members", sum(1 for member in role.members), True],
[
"Permissions",
f"```\n{repr_permissions or 'Nothing special.'}```", False
],
]
embed = self.bot.embed(ctx,
colour=discord.Color.from_rgb(*role_colour))
[embed.add_field(name=n, value=v, inline=i) for n, v, i in fields]
embed_list.append(embed)
def plot_subtitle(ax, text, fs, cfg):
"""
Add a title.
"""
color = utils.rgb_to_hex(cfg['highlight_colour'])
x = 1.0 if cfg['sidelabel'] == 'right' else 0.0
ax.text(x, -0.15, text, size=fs,
ha=cfg['sidelabel'],
va='top',
color=color,
)
ax.axis('off')
return ax
def by_name(color_name) -> 'html':
color = tikkurila_colors.color_by_name(color_name)
if color:
msg = 'Name "{}"; HEX: {}; RGB({}, {}, {})'.format(
color[3], utils.rgb_to_hex(color[0], color[1], color[2]), color[0],
color[1], color[2])
return render_template(
'color_by_name.html',
the_title=TITLE,
the_note='',
the_result='',
the_name_color0=msg,
the_color0=utils.rgb_to_hex(color[0], color[1], color[2]),
)
else:
msg = 'Color "{}" not found.'.format(color_name.upper())
return render_template(
'color.html',
the_title=TITLE,
the_note=color,
the_result=msg,
)
def plot_title(ax, text, fs, cfg):
"""
Add a title.
"""
x = 1.0 if cfg['sidelabel'] == 'right' else 0.0
color = utils.rgb_to_hex(cfg['highlight_colour'])
ax.text(
x,
0.0,
text,
size=fs,
ha=cfg['sidelabel'],
va='bottom',
color=color,
)
ax.axis('off')
return ax
def hueNormalizer(pathwaydict):
#Input:
#Processes:
#Output:
#Initialize variables:
#Variables initialized.
huesToBeNormalized = []
l = pathwaydict.keys()
keysToBeNormalized = fnmatch.filter(l, "*normalizedavg")
print("The keys being looked at are: ", keysToBeNormalized)
for keys in range(len(keysToBeNormalized)):
huesToBeNormalized.append(pathwaydict[keysToBeNormalized[keys]])
print("The huesToBeNormalized are: ", huesToBeNormalized)
largestavg = max(huesToBeNormalized)
smallestavg = min(huesToBeNormalized)
print("The largest hue avg is: ", largestavg, " and the smallest is: ",
smallestavg)
for entry in range(len(huesToBeNormalized)):
print(
"The node being looked at is: ",
keysToBeNormalized[entry].replace("normalizedavg",
"normalizedhueavg"))
print("The huesToBeNormalizedp[entry] is: ", huesToBeNormalized[entry])
pathwaydict[keysToBeNormalized[entry].replace(
"normalizedavg",
"normalizedhueavg")] = (huesToBeNormalized[entry] -
smallestavg) / (largestavg - smallestavg)
#print("The hue pre-processing values are: ", pathwaydict[keysToBeNormalized[entry].replace("normalizedavg","normalizedhueavg")], "and ints they are: ", int(255-(255*pathwaydict[keysToBeNormalized[entry].replace("normalizedavg","normalizedhueavg")]))) #DB
pathwaydict[keysToBeNormalized[entry].replace(
"normalizedavg", "huevalue")] = rgb_to_hex(
255,
int(255 - (255 * pathwaydict[keysToBeNormalized[entry].replace(
"normalizedavg", "normalizedhueavg")])),
int(255 - (255 * pathwaydict[keysToBeNormalized[entry].replace(
"normalizedavg", "normalizedhueavg")])))
return pathwaydict
def on_ok(self, e):
"""
Update the line to values from ui elements
"""
self.line.plot_line = self.cb_show_hide.GetValue()
self.line.intense_plot = self.cb_intense.GetValue()
self.line.thickness = self.thick_spin.GetValue()
try:
(r, g, b) = self.colour_picker.GetColour().Get()
self.line.rgb_tuple = (r, g, b)
self.line.flat_colour = rgb_to_hex((r, g, b))
self.line.sub_plot_tuples = self.line.plot_sub_plots(self.line.interpolated_results, self.line.interval, debug=False)
self.line.normalise()
self.line.debug_name = "Finish"
except:
print "No colour change"
WorldState.Instance().lamport_clock += 1
WorldState.Instance().push_state()
WorldState.Instance().reorder(WorldState.Instance().lamport_clock)
WorldState.Instance().refresh_animation()
self.Close()
def plot_sub_plots(self, results, interval, debug=False):
"""
Plots the sub plots and works out what colour the line should be
this is for colour intensity plot
"""
sub_plots = self.build_colour_plot_arrays(results, interval)
sub_plot_tuples = []
self.colour_change_points = []
for sub_plot in sub_plots:
count = 0
current = 0
while True:
if (sub_plot[count] is not None):
current = sub_plot[count]
break
count += 1
intensity = (((current - self.min) / float(1 + self.max - self.min)) * (_MAX_INTENSITY - _MIN_INTENSITY)) + _MIN_INTENSITY
alpha = intensity/255
new_colour = rgb_to_hex(rgba_to_rgb(self.rgb_tuple, alpha))
self.colour_change_points.append((count, new_colour))
sub_plot_tuples.append((sub_plot, new_colour))
self.seg_colour = self.colour_change_points[0][1]
return sub_plot_tuples
def main(target, cfg):
"""
Puts everything together.
"""
t0 = time.time()
#####################################################################
#
# READ SEGY
#
#####################################################################
if cfg['segy_library'].lower() == 'obspy':
s = Seismic.from_segy_with_obspy(target, params={'ndim': cfg['ndim']})
else:
s = Seismic.from_segy(target, params={'ndim': cfg['ndim']})
# Set the line and/or xline number.
try:
n, xl = cfg['number']
except:
n, xl = cfg['number'], 0.5
# Set the direction.
if (s.ndim) == 2:
direction = ['inline']
elif cfg['direction'].lower()[0] == 'i':
direction = ['inline']
elif cfg['direction'].lower()[0] in ['x', 'c']: # Allow 'crossline' too.
direction = ['xline']
elif cfg['direction'].lower()[0] == 't':
direction = ['tslice']
else:
direction = ['xline', 'inline']
# Get the data.
try:
ss = [
Seismic.from_seismic(s, n=n, direction=d)
for n, d in zip((n, xl), direction)
]
except IndexError:
# Perhaps misinterpreted 2D as 3D
s = Seismic.from_segy(target, params={'ndim': 2})
direction = ['inline']
ss = [
Seismic.from_seismic(s, n=n, direction=d)
for n, d in zip((n, xl), direction)
]
clip_val = np.percentile(s.data, cfg['percentile'])
if clip_val < 10:
fstr = '{:.3f}'
elif clip_val < 100:
fstr = '{:.2f}'
elif clip_val < 1000:
fstr = '{:.1f}'
else:
fstr = '{:.0f}'
# Notify user of parameters.
Notice.info("n_traces {}".format(s.ntraces))
Notice.info("n_samples {}".format(s.nsamples))
Notice.info("dt {}".format(s.dt))
Notice.info("t_start {}".format(s.tstart))
Notice.info("t_end {}".format(s.tend))
Notice.info("max_val " + fstr.format(np.amax(s.data)))
Notice.info("min_val " + fstr.format(np.amin(s.data)))
Notice.info("clip_val " + fstr.format(clip_val))
t1 = time.time()
Notice.ok("Read data in {:.1f} s".format(t1 - t0))
#####################################################################
#
# MAKE PLOT
#
#####################################################################
Notice.hr_header("Plotting")
# Plot size parameters.
wsl = 6 # Width of sidelabel, inches
mih = 11 # Minimum plot height, inches
fhh = 5 # File header box height, inches
m = 0.75 # basic unit of margins, inches
# Margins, CSS like: top, right, bottom, left.
mt, mr, mb, ml = m, 1.5 * m, m, 1.5 * m
mm = 2 * m # padded margin between seismic and label
# Determine plot dimensions. Kind of laborious and repetitive (see below).
if cfg['plot_width']:
seismic_width = cfg['plot_width'] - wsl - mm - ml - mr
tpi = max([s.ntraces for s in ss]) / seismic_width
else:
tpi = cfg['tpi']
if cfg['plot_height']:
seismic_height = max(
mih, cfg['plot_height']) - mb - 0.75 * (len(ss) - 1) - mt
seismic_height_raw = seismic_height / len(ss)
ips = seismic_height_raw / (s.tbasis[-1] - s.tbasis[0])
else:
ips = cfg['ips']
# Width is determined by seismic width, plus sidelabel, plus margins.
# Height is given by ips, but with a minimum of mih inches.
if 'tslice' in direction:
seismic_width = [s.ntraces / tpi for s in ss]
seismic_height_raw = max([s.nxlines for s in ss]) / tpi
else:
seismic_width = [s.ntraces / tpi for s in ss]
seismic_height_raw = ips * (s.tbasis[-1] - s.tbasis[0])
w = ml + max(seismic_width) + mm + wsl + mr # inches
seismic_height = len(ss) * seismic_height_raw
h_reqd = mb + seismic_height + 0.75 * (len(ss) - 1) + mt # inches
h = max(mih, h_reqd)
# Calculate where to start sidelabel and seismic data.
# Depends on whether sidelabel is on the left or right.
if cfg['sidelabel'] == 'right':
ssl = (ml + max(seismic_width) + mm) / w # Start of side label (ratio)
seismic_left = ml / w
else:
ssl = ml / w
seismic_left = (ml + wsl + mm) / w
adj = max(0, h - h_reqd) / 2
seismic_bottom = (mb / h) + adj / h
seismic_width_fraction = [sw / w for sw in seismic_width]
seismic_height_fraction = seismic_height_raw / h
# Publish some notices so user knows plot size.
Notice.info("plot width {:.2f} in".format(w))
Notice.info("plot height {:.2f} in".format(h))
# Make the figure.
fig = plt.figure(figsize=(w, h), facecolor='w')
# Set the tickformat.
tickfmt = mtick.FormatStrFormatter('%.0f')
# Could definitely do better for default fontsize than 10.
# Ideally would be adaptive to plot size.
cfg['fontsize'] = cfg['fontsize'] or 10
# Plot title.
if cfg['title']:
# Deal with Windows paths: \1 gets interpreted as a group by regex.
newt = re.sub(r'\\', '@@@@@', target)
temp = re.sub(r'_filename', newt, cfg['title'])
title = re.sub(r'@@@', r'\\', temp)
title_ax = fig.add_axes([ssl, 1 - mt / h, wsl / w, mt / h])
title_ax = plotter.plot_title(title_ax,
title,
fs=1.4 * cfg['fontsize'],
cfg=cfg)
# Plot title.
if cfg['subtitle']:
date = str(datetime.date.today())
subtitle = re.sub(r'_date', date, cfg['subtitle'])
subtitle_ax = fig.add_axes([ssl, 1 - mt / h, wsl / w, mt / h],
label='subtitle')
title_ax = plotter.plot_subtitle(subtitle_ax,
subtitle,
fs=0.75 * cfg['fontsize'],
cfg=cfg)
# Plot text header.
start = (h - 1.5 * mt - fhh) / h
head_ax = fig.add_axes([ssl, start, wsl / w, fhh / h])
head_ax = plotter.plot_header(head_ax,
s.header,
fs=9,
cfg=cfg,
version=__version__)
# Plot histogram.
# Params for histogram plot.
pady = 0.75 / h # 0.75 inch
padx = 0.75 / w # 0.75 inch
cstrip = 0.3 / h # color_strip height = 0.3 in
charth = 1.25 / h # height of charts = 1.25 in
chartw = wsl / w - mr / w - padx # or ml/w for left-hand sidelabel; same thing
chartx = (ssl + padx)
histy = 1.5 * mb / h + charth + pady
# Plot colourbar under histogram.
clrbar_ax = fig.add_axes([chartx, histy - cstrip, chartw, cstrip])
clrbar_ax = plotter.plot_colourbar(clrbar_ax, cmap=cfg['cmap'])
# Plot histogram itself.
hist_ax = fig.add_axes([chartx, histy, chartw, charth])
hist_ax = plotter.plot_histogram(hist_ax, s.data, tickfmt, cfg)
# Plot spectrum.
specy = 1.5 * mb / h
spec_ax = fig.add_axes([chartx, specy, chartw, charth])
try:
colour = utils.rgb_to_hex(cfg['highlight_colour'])
spec_ax = s.plot_spectrum(
ax=spec_ax,
tickfmt=tickfmt,
ntraces=20,
fontsize=cfg['fontsize'],
colour=colour,
)
except:
pass # No spectrum, oh well.
for i, line in enumerate(ss):
# Add the seismic axis.
ax = fig.add_axes([
seismic_left,
seismic_bottom + i * seismic_height_fraction + i * pady,
seismic_width_fraction[i], seismic_height_fraction
])
# Plot seismic data.
if cfg['display'].lower() in ['vd', 'varden', 'variable', 'both']:
im = ax.imshow(line.data.T,
cmap=cfg['cmap'],
clim=[-clip_val, clip_val],
extent=[
line.olineidx[0], line.olineidx[-1],
1000 * line.tbasis[-1], line.tbasis[0]
],
aspect='auto',
interpolation=cfg['interpolation'])
if np.argmin(seismic_width) == i:
cax = utils.add_subplot_axes(ax, [1.01, 0.02, 0.01, 0.2])
_ = plt.colorbar(im, cax=cax)
if cfg['display'].lower() in ['wiggle', 'both']:
ax = line.wiggle_plot(
cfg['number'],
direction,
ax=ax,
skip=cfg['skip'],
gain=cfg['gain'],
rgb=cfg['colour'],
alpha=cfg['opacity'],
lw=cfg['lineweight'],
)
valid = ['vd', 'varden', 'variable', 'wiggle', 'both']
if cfg['display'].lower() not in valid:
Notice.fail("You must specify the display: wiggle, vd, both.")
return
# Seismic axis annotations.
ax.set_ylabel(utils.LABELS[line.ylabel], fontsize=cfg['fontsize'])
ax.set_xlabel(utils.LABELS[line.xlabel],
fontsize=cfg['fontsize'],
ha='center')
ax.tick_params(axis='both', labelsize=cfg['fontsize'] - 2)
ax.xaxis.set_major_formatter(tickfmt)
ax.yaxis.set_major_formatter(tickfmt)
if ('tslice' not in direction):
ax.set_ylim(1000 * cfg['trange'][1] or 1000 * line.tbasis[-1],
1000 * cfg['trange'][0])
# Crossing point. Will only work for non-arb lines.
try:
ax.axvline(ss[i - 1].slineidx[0],
c=utils.rgb_to_hex(cfg['highlight_colour']),
alpha=0.5)
except IndexError:
pass # Nevermind.
# Grid, optional.
if cfg['grid_time'] or cfg['grid_traces']:
ax.grid()
for l in ax.get_xgridlines():
l.set_color(utils.rgb_to_hex(cfg['grid_colour']))
l.set_linestyle('-')
if cfg['grid_traces']:
l.set_linewidth(1)
else:
l.set_linewidth(0)
l.set_alpha(min(1, cfg['grid_alpha']))
for l in ax.get_ygridlines():
l.set_color(utils.rgb_to_hex(cfg['grid_colour']))
l.set_linestyle('-')
if cfg['grid_time']:
if 'tslice' in direction:
l.set_linewidth(1)
else:
l.set_linewidth(1.4)
else:
l.set_linewidth(0)
l.set_alpha(min(1, 2 * cfg['grid_alpha']))
# Watermark.
if cfg['watermark_text']:
ax = plotter.watermark_seismic(ax, cfg)
# Make parasitic (top) axis for labeling CDP number.
if (s.data.ndim > 2) and ('tslice' not in direction):
ylim = ax.get_ylim()
par1 = ax.twiny()
par1.spines["top"].set_position(("axes", 1.0))
par1.plot(line.slineidx, np.zeros_like(line.slineidx), alpha=0)
par1.set_xlabel(utils.LABELS[line.slabel],
fontsize=cfg['fontsize'])
par1.set_ylim(ylim)
# Adjust ticks
tx = par1.get_xticks()
newtx = [
line.slineidx[len(line.slineidx) * (i // len(tx))]
for i, _ in enumerate(tx)
]
par1.set_xticklabels(newtx, fontsize=cfg['fontsize'] - 2)
t2 = time.time()
Notice.ok("Built plot in {:.1f} s".format(t2 - t1))
#####################################################################
#
# SAVE FILE
#
#####################################################################
Notice.hr_header("Saving")
dname, fname, ext = utils.path_bits(target)
outfile = cfg['outfile'] or ''
if not os.path.splitext(outfile)[1]:
outfile = os.path.join(cfg['outfile'] or dname, fname + '.png')
fig.savefig(outfile)
t3 = time.time()
Notice.info("output file {}".format(outfile))
Notice.ok("Saved output in {:.1f} s".format(t3 - t2))
if cfg['stain_paper'] or cfg['coffee_rings'] or cfg['distort'] or cfg[
'scribble']:
fname = os.path.splitext(outfile)[0] + ".stupid.png"
fig.savefig(fname)
else:
return
#####################################################################
#
# SAVE STUPID FILE
#
#####################################################################
Notice.hr_header("Applying the stupidity")
stupid_image = Image.open(fname)
if cfg['stain_paper']:
utils.stain_paper(stupid_image)
utils.add_rings(stupid_image, cfg['coffee_rings'])
if cfg['scribble']:
utils.add_scribble(stupid_image)
# Trick to remove remaining semi-transparent pixels.
result = Image.new("RGB", stupid_image.size, (255, 255, 255))
result.paste(stupid_image)
result.save(fname)
t4 = time.time()
Notice.info("output file {}".format(fname))
Notice.ok("Saved stupidity in {:.1f} s".format(t4 - t3))
return
def fbget_PerPathwayInfo(pathwayNodes, pairedcases):
#Input: Nodes from NetPath for a particular pathway
#Process: Produces fbget data for every single node in the pathway, puts the data into a dictionary for that node that is formatted as "[Node][output]" in a string.
#Output: An array>array containing the information in the text files separated by column and line.
#Initialize variables
pathwaydict = {
} #Holds all the fbget information per node in a dictionary. Processed information is accessible by "[Node][output]" - which is the node, and the type of information in one string.
#Variables initialized.
for node in range(len(pathwayNodes)):
#For determining what kind of data you'd like to pull from firebrowse - for gene expression data, 2 means expression_log2, while 3 means the z-score of that data point.
print(fbget.mrnaseq(gene=pathwayNodes[node][2], cohort="coad"))
print("The node currently being analyzed is: " + pathwayNodes[node][2])
#Pulls the mRNA sequencing activity
fbget_Output = fbget_Reader(
fbget.mrnaseq(gene=pathwayNodes[node][2],
cohort="coad",
page_size=2000), {2})
#Pulls out patient ID and sample type.
fbget_Patient = fbget_Reader(
fbget.mrnaseq(gene=pathwayNodes[node][2],
cohort="coad",
page_size=2000), {0, 5})
#Production of the information dictionary pathwaydict
pathwaydict[pathwayNodes[node][2]] = fbget_Output
pathwaydict[(pathwayNodes[node][2]) + "ID"] = fbget_Patient
if pairedcases == True:
Ndict, Tdict = fbget_PatientPairer(pathwaydict,
((pathwayNodes[node][2])))
Narray = list(itertools.chain.from_iterable(Ndict.values()))
Tarray = list(itertools.chain.from_iterable(Tdict.values()))
#Performing a t-test, and then other statistical analysis.
print("The amount of normal samples is: ", len(Narray))
print("The amount of tumor samples is: ", len(Tarray))
tstat, tsignificance = stats.ttest_ind(Narray,
Tarray,
equal_var=True)
if tsignificance < 0.05:
print("The difference is significant for ",
pathwayNodes[node][2])
pathwaydict[(pathwayNodes[node][2]) + "tstat"] = tstat
pathwaydict[(pathwayNodes[node][2]) +
"tsignificance"] = tsignificance
print("The t-test results for ", pathwayNodes[node][2], "are ",
pathwaydict[(pathwayNodes[node][2]) + "tstat"], " and ",
pathwaydict[(pathwayNodes[node][2]) + "tsignificance"])
print("Normalizing Narray: ")
fbget_Normalizing(Narray, False)
print("Normalizing Tarray: ")
fbget_Normalizing(Tarray, False)
#Nodes in a pathway, and then eventually nodes for an entire type of cancer on the pathways it has been seen to affect.
normalizedvalue, avg, normalizedavg, zscores = fbget_Normalizing(
fbget_Output, True)
pathwaydict[(pathwayNodes[node][2]) +
"normalizedvalue"] = normalizedvalue
pathwaydict[(pathwayNodes[node][2]) + "avg"] = avg
pathwaydict[(pathwayNodes[node][2]) + "normalizedavg"] = normalizedavg
pathwaydict[(pathwayNodes[node][2]) + "zscores"] = zscores
if tsignificance < 0.01:
pathwaydict[(pathwayNodes[node][2]) + "huevalue"] = rgb_to_hex(
255, int(255 * tsignificance), int(255 * tsignificance))
else:
pathwaydict[(pathwayNodes[node][2]) + "huevalue"] = rgb_to_hex(
255, int(255), int(255))
#e.g. To access WNT7's normalizedavg, use the value "pathwaydict["WNT7normalizedavg"]""
#print(pathwaydict["WNT7Anormalizedavg"]) #DB
return pathwaydict
def subclass_init(self, loc=None):
super(SimHerbivore, self).subclass_init(loc)
self.energy = 40
self.color = rgb_to_hex(self.r, self.g, self.b)
self.age = 0
def subclass_init(self, loc=None):
super(SimPlant, self).subclass_init(loc)
self.energy = 0
self.color = rgb_to_hex(self.r, self.g, self.b)
self.size = 0
def plot_line(self, line):
"""
Decides, for each line, how we're going to plot, normal or with intensities
"""
if line.plot_line:
if not WorldState.Instance().session_dict['normalised']:
if not line.intense_plot:
self.axes.plot(line.original_time, line.original_results, label=line.species, color=rgb_to_hex(line.rgb_tuple), alpha=1, lw=line.thickness)
else:
for (sub_plot, new_colour) in line.sub_plot_tuples:
self.axes.plot(line.interpolated_time, sub_plot, color=new_colour, lw=line.thickness)
else:
if not line.intense_plot:
self.axes.plot(line.original_time, line.normalised_results, label=line.species, color=rgb_to_hex(line.rgb_tuple), alpha=1, lw=line.thickness)
else:
for (sub_plot, new_colour) in line.normalised_sub_plots:
self.axes.plot(line.interpolated_time, sub_plot, color=new_colour, lw=line.thickness)
def plot_histogram(ax, data, tickfmt, cfg):
"""
Plot a histogram of amplitude values.
"""
fs = cfg['fontsize']
percentile = cfg['percentile']
data = np.array(data)
datamax = np.amax(data)
datamin = np.amin(data)
datamean = np.nanmean(data)
largest = max(datamax, abs(datamin))
clip_val = np.percentile(data, percentile)
ax.patch.set_alpha(0.0)
color = utils.rgb_to_hex(cfg['highlight_colour'])
y, x, _ = ax.hist(np.ravel(data),
bins=int(100.0 / (clip_val / largest)),
alpha=0.6,
color=color,
lw=0)
ax.set_xlim(-clip_val, clip_val)
ax.set_xticklabels(ax.get_xticks(), fontsize=fs - 4)
ax.set_xlabel('amplitude', fontsize=fs - 4)
ax.xaxis.set_label_coords(0.5, -0.12)
ax.set_ylim([0, y.max()])
ax.set_yticks(np.linspace(0, y.max(), 6))
ax.set_ylabel('percentage of samples', fontsize=fs - 4)
ax.tick_params(axis='x', pad=25)
ax.xaxis.labelpad = 25
ticks = ax.get_yticks().tolist() # ytick labels
percentages = 100 * np.array(ticks) / data.size
labels = []
for label in percentages:
labels.append("{:.2f}".format(label))
ax.set_yticklabels(labels, fontsize=fs - 4)
ax.xaxis.set_major_formatter(tickfmt)
if datamax < 1:
statstring = "\nMinimum: {:.4f}\nMean: {:.4f}\nMaximum: {:.4f}".format(
datamin, datamean, datamax)
statstring += "\n{:.1f} percentile: {:.4f}".format(
percentile, clip_val)
elif datamax < 10:
statstring = "\nMinimum: {:.2f}\nMean: {:.2f}\nMaximum: {:.2f}".format(
datamin, datamean, datamax)
statstring += "\n{:.1f} percentile: {:.2f}".format(
percentile, clip_val)
elif datamax < 100:
statstring = "\nMinimum: {:.1f}\nMean: {:.1f}\nMaximum: {:.1f}".format(
datamin, datamean, datamax)
statstring += "\n{:.1f} percentile: {:.1f}".format(
percentile, clip_val)
else:
statstring = "\nMinimum: {:.0f}\nMean: {:.0f}\nMaximum: {:.0f}".format(
datamin, datamean, datamax)
statstring += "\n{:.1f} percentile: ±{:.0f}".format(
percentile, clip_val)
ax.text(.98,
.95,
'AMPLITUDE HISTOGRAM',
horizontalalignment='right',
verticalalignment='top',
fontweight='bold',
color=utils.rgb_to_hex(cfg['highlight_colour']),
transform=ax.transAxes,
fontsize=fs - 3)
ax.text(.98,
.95,
statstring,
horizontalalignment='right',
verticalalignment='top',
transform=ax.transAxes,
fontsize=fs - 3)
ax.set_alpha(0)
ax.grid()
gridlines = ax.get_xgridlines() + ax.get_ygridlines()
for line in gridlines:
line.set_linestyle('-')
line.set_alpha(0.2)
return ax