def save_plot(self, fig, axes, **kwargs):
# Parameters #
self.params = {}
for key in self.default_params:
if key in kwargs: self.params[key] = kwargs[key]
elif hasattr(self, key): self.params[key] = getattr(self, key)
elif self.default_params[key] is not None: self.params[key] = self.default_params[key]
# Backwards compatibility #
if kwargs.get('x_log', False): self.params['x_scale'] = 'symlog'
if kwargs.get('y_log', False): self.params['y_scale'] = 'symlog'
# Log #
if 'x_scale' in self.params: axes.set_xscale(self.params['x_scale'])
if 'y_scale' in self.params: axes.set_yscale(self.params['y_scale'])
# Axis limits #
if 'x_min' in self.params: axes.set_xlim(self.params['x_min'], axes.get_xlim()[1])
if 'x_max' in self.params: axes.set_xlim(axes.get_xlim()[0], self.params['x_max'])
if 'y_min' in self.params: axes.set_xlim(self.params['y_min'], axes.get_ylim()[1])
if 'y_max' in self.params: axes.set_xlim(axes.get_ylim()[0], self.params['y_max'])
# Title #
title = self.params.get('title', False)
if title: axes.set_title(title)
# Axes labels #
if self.params.get('x_label'): axes.set_xlabel(self.params['x_label'])
if self.params.get('y_label'): axes.set_ylabel(self.params['y_label'])
# Adjust #
fig.set_figwidth(self.params['width'])
fig.set_figheight(self.params['height'])
fig.subplots_adjust(hspace=0.0, bottom = self.params['bottom'], top = self.params['top'],
left = self.params['left'], right = self.params['right'])
# Grid #
axes.xaxis.grid(self.params['x_grid'])
axes.yaxis.grid(self.params['y_grid'])
# Data and source extra text #
if hasattr(self, 'dev_mode') and self.dev_mode is True:
fig.text(0.99, 0.98, time.asctime(), horizontalalignment='right')
job_name = os.environ.get('SLURM_JOB_NAME', 'Unnamed')
user_msg = 'user: %s, job: %s' % (getpass.getuser(), job_name)
fig.text(0.01, 0.98, user_msg, horizontalalignment='left')
# Nice digit grouping #
if 'x' in self.params['sep']:
separate = lambda x,pos: split_thousands(x)
axes.xaxis.set_major_formatter(matplotlib.ticker.FuncFormatter(separate))
if 'y' in self.params['sep']:
separate = lambda y,pos: split_thousands(y)
axes.yaxis.set_major_formatter(matplotlib.ticker.FuncFormatter(separate))
# Add custom labels #
if 'x_labels' in self.params: axes.set_xticklabels(self.params['x_labels'])
if 'x_labels_rot' in self.params: pyplot.setp(axes.xaxis.get_majorticklabels(), rotation=self.params['x_labels_rot'])
# Possibility to overwrite path #
if 'path' in self.params: path = FilePath(self.params['path'])
elif hasattr(self, 'path'): path = FilePath(self.path)
else: path = FilePath(self.short_name + '.pdf')
# Save it as different formats #
for ext in self.params['formats']: fig.savefig(path.replace_extension(ext))
def __init__(self, parent=None, base_dir=None, short_name=None):
# Save parent #
self.parent = parent
# Base dir #
if base_dir is None: self.base_dir = self.parent.p.graphs_dir
else: self.base_dir = base_dir
# Short name #
if short_name: self.short_name = short_name
if not hasattr(self, 'short_name'): self.short_name = 'graph'
# Paths #
self.path = FilePath(self.base_dir + self.short_name + '.pdf')
def download_from_url(source, destination, progress=False, uncompress=True):
"""Download a file from an URL and place it somewhere. Like wget.
Uses requests and tqdm to display progress if you want.
By default it will uncompress files."""
# Modules #
from tqdm import tqdm
import requests
from autopaths import FilePath
# Check destination exists #
destination = FilePath(destination)
destination.directory.create_if_not_exists()
# Over HTTP #
response = requests.get(source, stream=True)
total_size = int(response.headers.get('content-length'))
block_size = total_size / 1024
# Do it #
with open(destination, "wb") as handle:
if progress:
for data in tqdm(response.iter_content(chunk_size=block_size),
total=1024):
handle.write(data)
else:
for data in response.iter_content(chunk_size=block_size):
handle.write(data)
# Uncompress #
if uncompress:
with open(destination) as f:
header = f.read(4)
if header == "PK\x03\x04": unzip(destination, inplace=True)
# Add other compression formats here
# Return #
return destination
def __new__(cls, path=None, content=None, **kwargs):
handle = open(path, 'w') if path else tempfile.NamedTemporaryFile(delete=False, **kwargs)
if content: handle.write(content)
handle.close()
return FilePath.__new__(cls, handle.name)
def __new__(cls, path=None, content=None, **kwargs):
handle = open(path, 'w') if path else tempfile.NamedTemporaryFile(delete=False, **kwargs)
if content: handle.write(content)
handle.close()
return FilePath.__new__(cls, handle.name)
class Graph(object):
width = 12.0
height = 7.0
bottom = 0.14
top = 0.93
left = 0.06
right = 0.98
formats = ('pdf',)
def __nonzero__(self): return self.path.__nonzero__()
def __init__(self, parent=None, base_dir=None, short_name=None):
# Save parent #
self.parent = parent
# Base dir #
if base_dir is None: self.base_dir = self.parent.p.graphs_dir
else: self.base_dir = base_dir
# Short name #
if short_name: self.short_name = short_name
if not hasattr(self, 'short_name'): self.short_name = 'graph'
# Paths #
self.path = FilePath(self.base_dir + self.short_name + '.pdf')
def __call__(self, *args, **kwatgs):
"""Plot the graph if it doesn't exist. Then return the path to it."""
if not self: self.plot(*args, **kwatgs)
return self.path
def save_plot(self, fig, axes, width=None, height=None, bottom=None, top=None, left=None, right=None, sep=()):
# Attributes or parameters #
w = width if width != None else self.width
h = height if height != None else self.height
b = bottom if bottom != None else self.bottom
t = top if top != None else self.top
l = left if left != None else self.left
r = right if right != None else self.right
# Adjust #
fig.set_figwidth(w)
fig.set_figheight(h)
fig.subplots_adjust(hspace=0.0, bottom=b, top=t, left=l, right=r)
# Data and source #
if hasattr(self, 'dev_mode'):
fig.text(0.99, 0.98, time.asctime(), horizontalalignment='right')
job_name = os.environ.get('SLURM_JOB_NAME', 'Unnamed')
user_msg = 'user: %s, job: %s' % (getpass.getuser(), job_name)
fig.text(0.01, 0.98, user_msg, horizontalalignment='left')
# Nice digit grouping #
if 'x' in sep:
seperate = lambda x,pos: split_thousands(x)
axes.xaxis.set_major_formatter(matplotlib.ticker.FuncFormatter(seperate))
if 'y' in sep:
seperate = lambda y,pos: split_thousands(y)
axes.yaxis.set_major_formatter(matplotlib.ticker.FuncFormatter(seperate))
# Save it as different formats #
for ext in self.formats: fig.savefig(self.path.replace_extension(ext))
def plot(self):
"""An example plot function. You have to subclass this method."""
fig = pyplot.figure()
axes = fig.add_subplot(111)
axes.plot([0,1,10,1000], [0,1,2,3], 'ro')
axes.set_title("Rarefaction curve of the diversity estimate")
axes.set_xlabel("Sequences rarefied down to this many sequences")
axes.set_ylabel("The diversity estimate")
axes.yaxis.grid(True)
axes.set_xscale('symlog')
axes.set_xlim(0, axes.get_xlim()[1])
self.save_plot(fig, axes, sep=('x',))
pyplot.close(fig)
def save_anim(self, fig, animate, init, bitrate=10000, fps=30):
"""Not functional -- TODO"""
from matplotlib import animation
anim = animation.FuncAnimation(fig, animate, init_func=init, frames=360, interval=20)
FFMpegWriter = animation.writers['ffmpeg']
writer = FFMpegWriter(bitrate= bitrate, fps=fps)
# Save #
self.avi_path = self.base_dir + self.short_name + '.avi'
anim.save(self.avi_path, writer=writer, codec='x264')