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836d06e
adding movie
briandrawert Feb 21, 2021
94a1fe1
Merge pull request #70 from StochSS/timeout-and-str
BryanRumsey Feb 25, 2021
fa99a72
Added timestep_size to the timespan function. Closes #74
BryanRumsey Mar 2, 2021
7583ce7
Added 'add_mesh' function that will set a models mesh and the list of…
BryanRumsey Mar 2, 2021
8542d4d
Fixed interation bug in the initial conditions section of the models …
BryanRumsey Mar 2, 2021
fa5b87c
Added function that read in a shochss domain and convert it to a Spat…
BryanRumsey Mar 2, 2021
81d52f6
adding spatial birth death model, shows error for #78
briandrawert Mar 3, 2021
cae4990
Merge pull request #81 from StochSS/spatial_birth_death_model
makdl Mar 3, 2021
ccf2496
Fixed error reporting typo.
BryanRumsey Mar 5, 2021
004f0a3
Fixed bug the was assigning the wrong name for ploting species to the…
BryanRumsey Mar 5, 2021
4fbc402
Implemented Result eq and ne
makdl Mar 6, 2021
3802ed4
Re-implemented solver seed tests
makdl Mar 6, 2021
b214853
Replace diffusion model with simplier model
makdl Mar 6, 2021
d6357e3
Renamed GitHub Actions unit test job
makdl Mar 6, 2021
182cfc1
Removed unused imports & whitespace
makdl Mar 6, 2021
d1cc553
Removed unneeded print statement
makdl Mar 6, 2021
3b626bd
Clarify license information
makdl Mar 6, 2021
6b7ba2e
Updated URLS & license clarification
makdl Mar 6, 2021
54079af
Added AUTHORS file, sorted alphabetically
makdl Mar 6, 2021
1db06d0
Updated RELEASE_NOTES & more URLS
makdl Mar 6, 2021
3d5943f
Replace Python2 PATH with Python3
makdl Mar 6, 2021
7bc2673
Remove mistakenly commited debug script
makdl Mar 6, 2021
b6b4c91
Implemented regex filter for propensity filenames
makdl Mar 6, 2021
c3d2a93
Merge pull request #86 from StochSS/sanitize_model_names
briandrawert Mar 6, 2021
a7ba1e1
Re-implemented pickle tests & pickling
makdl Mar 6, 2021
175ebc6
Merge pull request #85 from StochSS/clarify_license
briandrawert Mar 6, 2021
87f27b9
Removed typo
makdl Mar 6, 2021
8daf04d
Merge pull request #83 from StochSS/ploting-bugs
briandrawert Mar 6, 2021
311fda0
Merge pull request #80 from StochSS/stochss_domain
briandrawert Mar 6, 2021
dfda87b
Merge pull request #84 from StochSS/test_updates1
briandrawert Mar 6, 2021
f6641b7
Merge pull request #79 from StochSS/timespan-update
briandrawert Mar 6, 2021
2533190
Fixed typo in the model class str function.
BryanRumsey Mar 8, 2021
a16b03f
Merge pull request #91 from StochSS/str-typo
makdl Mar 8, 2021
091dedd
Removed Result Dict inheritance
makdl Mar 8, 2021
cd9609b
Added Result timeout flag
makdl Mar 8, 2021
7274994
Implemented results output pickling
makdl Mar 9, 2021
0aa5173
Merge pull request #92 from StochSS/remove_dict_inherit
BryanRumsey Mar 9, 2021
d5382b9
Merge pull request #93 from StochSS/pickle_results_dir
BryanRumsey Mar 9, 2021
56bdbb2
Update RELEASE_NOTES
makdl Mar 9, 2021
d2b27e4
Update __version__.py
makdl Mar 9, 2021
6a6131e
Merge pull request #94 from StochSS/beta-0.6.1
BryanRumsey Mar 9, 2021
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Removed unused imports & whitespace
  • Loading branch information
makdl committed Mar 6, 2021
commit 182cfc1946ba8dbb0ea7cd00e2ebf7cd69ede450
27 changes: 7 additions & 20 deletions spatialpy/Result.py
Original file line number Diff line number Diff line change
@@ -1,28 +1,14 @@
import filecmp
import math
import os
import re
import pickle
import shutil
import subprocess
import sys
import tempfile
import types
import warnings
import uuid
import filecmp

import numpy
import scipy.io
import scipy.sparse

from spatialpy.VTKReader import VTKReader
from spatialpy.Model import *

import inspect

import pickle
import json
import math


from spatialpy.VTKReader import VTKReader

common_rgb_values=['#1f77b4','#ff7f0e','#2ca02c','#d62728','#9467bd','#8c564b','#e377c2','#7f7f7f',
'#bcbd22','#17becf','#ff0000','#00ff00','#0000ff','#ffff00','#00ffff','#ff00ff',
Expand Down Expand Up @@ -188,6 +174,7 @@ def get_species(self, species, timepoints=None, concentration=False, determinist
#t_index_arr = numpy.linspace(0,self.model.num_timesteps,
# num=self.model.num_timesteps+1, dtype=int)
t_index_arr = self.get_timespan();
# Should this ; be here? ^

if timepoints is not None:
if isinstance(timepoints,float):
Expand Down Expand Up @@ -289,7 +276,7 @@ def plot_species(self, species, t_ndx=0, concentration=False, deterministic=Fals

if use_matplotlib:
import matplotlib.pyplot as plt

if (deterministic or not concentration):
d = data[spec_name]
else:
Expand Down Expand Up @@ -528,7 +515,7 @@ def plot_property(self, property_name, t_ndx=0, p_ndx=0, width=500, height=500,

if use_matplotlib:
import matplotlib.pyplot as plt

if (property_name == 'v'):
d = data[property_name]
d = [d[i][p_ndx] for i in range(0,len(d))]
Expand Down