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VTK lib selection #117

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Merged
BryanRumsey merged 2 commits into from
Jun 15, 2021
Merged

VTK lib selection #117

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f78940d
Prefer our VTKReader: bug reading D[] results as array in official
makdl Jun 14, 2021
854d1d5
Variables might need to be renamed: PR #116 bug?
makdl Jun 14, 2021
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10 changes: 5 additions & 5 deletions spatialpy/Result.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,13 +9,12 @@
import numpy

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

try:
import vtk
except ImportError as e:
print('''The Python package 'vtk' is not installed. Using integrated VTK reader. This is significantly
slower than the official VTK package.''')
from spatialpy.VTKReader import VTKReader
pass

common_rgb_values=['#1f77b4','#ff7f0e','#2ca02c','#d62728','#9467bd','#8c564b','#e377c2','#7f7f7f',
'#bcbd22','#17becf','#ff0000','#00ff00','#0000ff','#ffff00','#00ffff','#ff00ff',
Expand Down Expand Up @@ -68,6 +67,7 @@ def __init__(self, model=None, result_dir=None):
self.stdout = None
self.stderr = None
self.timeout = False
self.official_vtk = False
self.result_dir = result_dir


Expand Down Expand Up @@ -183,7 +183,7 @@ def read_step(self, step_num, debug=False):
if debug:
print("read_step({0}) opening '{1}'".format(step_num, filename))

if 'vtk' in sys.modules:
if self.official_vtk:
reader = vtk.vtkGenericDataObjectReader()
reader.SetFileName(filename)
reader.Update()
Expand Down Expand Up @@ -380,7 +380,7 @@ def plot_species(self, species, t_ndx=0, concentration=False, deterministic=Fals
if colormap is None:
colormap = "viridis"

plt.figure(figsize=(mpl_width,mpl_height))
plt.figure(figsize=(width, height))
plt.scatter(points[:,0],points[:,1],c=d,cmap=colormap)
plt.axis('scaled')
plt.colorbar()
Expand Down