def __init__(self, f, group_name, postfix, params): self.fn = f.filename self.postfix = postfix self.group_name = group_name if identifycluster.getname() == 'snowden': my_threads = 16 else: my_threads = 4 # self.params = dict( # res=(1400,1400), # aa=4, # colored_slice=True, # out_alpha=True, # num_threads=my_threads, # temp_file_dir = '/tmp', # cam = 'topdown' # ) # self.params.update(params) params.threads = my_threads self.params = params self.runtime_and_mem = estimateRuntimeAndMemory(f[self.group_name])
import qsub import third_party import third_party.ffmpy import collections import shutil #import krebs.povrayRenderVessels from krebs.povrayRenderVessels import addVesselTree, cm_redblue from krebs.povrayEasy import * import krebs.povrayRenderSettings from krebsjobs.submitPovrayRender import RenderJob from krebsjobs.submitPovrayRender import clientfunc import datetime import identifycluster if (identifycluster.getname() == 'snowden'): FFMPEG_BIN = "ffmpeg_latest" else: FFMPEG_BIN = "ffmpeg" # on Linux ans Mac OS colors = [(0., 0.2, 0., 0.), (1., 0., 1.0, 0.)] cm_gf = matplotlib.colors.LinearSegmentedColormap('', { 'red': [(x, r, r) for (x, r, g, b) in colors], 'green': [(x, g, g) for (x, r, g, b) in colors], 'blue': [(x, b, b) for (x, r, g, b) in colors], }, N=256, gamma=1.) def renderSliceWithDistribution(vesselgroup, imagefn, options):
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>. ''' import os import numpy as np import matplotlib import identifycluster if (identifycluster.getname()=='snowden' or identifycluster.getname()=='durga'): matplotlib.use('agg') ''' pay attention: most likely this functions are imported somewhere else''' #from mpl_toolkits.axes_grid1.inset_locator import inset_axes from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar #from mpl_toolkits.axes_grid.anchored_artists import AnchoredText ''' needed to plot iff and drug stuff ''' from mpl_toolkits.axes_grid1 import make_axes_locatable import matplotlib.gridspec as gridspec from matplotlib.offsetbox import AnchoredOffsetbox, AuxTransformBox, VPacker,\ TextArea, DrawingArea class PdfWriter(object): def __init__(self, filename, multipage=True, absorbExtension_ = True): import matplotlib.backends.backend_pdf as be
from os.path import join, basename, dirname, splitext import os import h5py import numpy as np import collections import posixpath import fnmatch import posixpath import md5 import cPickle import uuid import decimal import identifycluster if identifycluster.getname() == 'snowden': cluster_threads = 16 elif identifycluster.getname() == 'durga': cluster_threads = 6 else: cluster_threads = 4 commonprefix = posixpath.commonprefix def commonsuffix(l): rev = map(lambda s: s[::-1], l) ret = commonprefix(rev) ret = ret[::-1] return ret