def make_binder(path):
src_path = os.path.abspath(path)
sim_paths_list = find_sim_dirs(src_path)
for path in sim_paths_list:
sim_name = os.path.split(path)[1]
make_notebook(path, sim_name)
if len(sim_paths_list) == 1 and sim_paths_list[0] == src_path:
files = os.listdir(src_path)
files = [os.path.join(src_path, f) for f in files]
mkdir(os.path.join(src_path, sim_name))
could_not_copy = []
for f in files:
try:
copy(f, os.path.join(src_path, sim_name))
except BaseException as exc:
could_not_copy.append([f, exc])
continue
os.remove(f)
if len(could_not_copy) != 0:
print("Could not copy the following files:\n")
for f in could_not_copy:
print('file: ', f[0])
print('error: ', f[1], '\n')
_write_readme_requrements(src_path)
def write_vtk(self, array_name, props):
# ceck if it is possible
if not TVTK:
raise RuntimeError("Cannot generate VTK output!")
# check if the array is legal
if array_name not in self.array_dict.keys():
raise RuntimeError("Array %s not defined" % array_name)
# create a list of props
if type(props) != list:
props = [props]
# create an output folder for the vtk files
dirname = path.join(self.dirname, "vtk")
utils.mkdir(dirname)
array = self.array_dict[array_name]
num_particles = array.num_real_particles
# save the points
points = np.zeros(shape=(num_particles, 3))
points[:, 0] = array.z
points[:, 1] = array.y
points[:, 2] = array.x
mesh = tvtk.PolyData(points=points)
# add the scalar props
for prop in props:
if prop == "vmag":
u, v, w = array.get("u", "v", "w")
numpy_array = np.sqrt(u ** 2 + v ** 2 + w ** 2)
else:
numpy_array = array.get(prop)
vtkarray = array2vtk(numpy_array)
vtkarray.SetName(prop)
# add the array as point data
mesh.point_data.add_array(vtkarray)
# set the last prop as the active scalar
mesh.point_data.set_active_scalars(props[-1])
# spit it out
if self.fileno is None:
_fname = "%s" % (array_name)
else:
_fname = "%s_%03d" % (array_name, self.fileno)
self._write_vtk_snapshot(mesh, dirname, _fname)
def write_vtk(self, array_name, props):
# ceck if it is possible
if not TVTK:
raise RuntimeError('Cannot generate VTK output!')
# check if the array is legal
if array_name not in list(self.array_dict.keys()):
raise RuntimeError('Array %s not defined' % array_name)
# create a list of props
if type(props) != list:
props = [props]
# create an output folder for the vtk files
dirname = path.join(self.dirname, 'vtk')
utils.mkdir(dirname)
array = self.array_dict[array_name]
num_particles = array.num_real_particles
# save the points
points = np.zeros(shape=(num_particles, 3))
points[:, 0] = array.z
points[:, 1] = array.y
points[:, 2] = array.x
mesh = tvtk.PolyData(points=points)
# add the scalar props
for prop in props:
if prop == 'vmag':
u, v, w = array.get('u', 'v', 'w')
numpy_array = np.sqrt(u**2 + v**2 + w**2)
else:
numpy_array = array.get(prop)
vtkarray = array2vtk(numpy_array)
vtkarray.SetName(prop)
# add the array as point data
mesh.point_data.add_array(vtkarray)
# set the last prop as the active scalar
mesh.point_data.set_active_scalars(props[-1])
# spit it out
if self.fileno is None:
_fname = '%s' % (array_name)
else:
_fname = '%s_%03d' % (array_name, self.fileno)
self._write_vtk_snapshot(mesh, dirname, _fname)
def write_vtk(self, array_name, props):
if not TVTK:
return
# create a list of props
if type(props) != list:
props = [props]
# create an output folder for the vtk files
dirname = path.join(self.dirname, "vtk")
utils.mkdir(dirname)
nfiles = self.nfiles
for i in range(self.start, nfiles):
f = self.files[i]
data = utils.load(f)
array = data["arrays"][array_name]
num_particles = array.num_real_particles
# save the points
points = np.zeros(shape=(num_particles, 3))
points[:, 0] = array.z
points[:, 1] = array.y
points[:, 2] = array.x
mesh = tvtk.PolyData(points=points)
# add the scalar props
for prop in props:
if prop == "vmag":
u, v, w = array.get("u", "v", "w")
numpy_array = np.sqrt(u ** 2 + v ** 2 + w ** 2)
else:
numpy_array = array.get(prop)
vtkarray = array2vtk(numpy_array)
vtkarray.SetName(prop)
# add the array as point data
mesh.point_data.add_array(vtkarray)
# set the last prop as the active scalar
mesh.point_data.set_active_scalars(props[-1])
# spit it out
fileno = data["solver_data"]["count"]
_fname = self.fname + "_%s_%s" % (array_name, fileno)
self._write_vtk_snapshot(mesh, dirname, _fname)
def write_vtk(self, array_name, props):
if not TVTK:
return
# create a list of props
if type(props) != list:
props = [props]
# create an output folder for the vtk files
dirname = path.join(self.dirname, 'vtk')
utils.mkdir(dirname)
nfiles = self.nfiles
for i in range(self.start, nfiles):
f = self.files[i]
data = utils.load(f)
array = data['arrays'][array_name]
num_particles = array.num_real_particles
# save the points
points = np.zeros(shape=(num_particles, 3))
points[:, 0] = array.z
points[:, 1] = array.y
points[:, 2] = array.x
mesh = tvtk.PolyData(points=points)
# add the scalar props
for prop in props:
if prop == 'vmag':
u, v, w = array.get('u', 'v', 'w')
numpy_array = np.sqrt(u**2 + v**2 + w**2)
else:
numpy_array = array.get(prop)
vtkarray = array2vtk(numpy_array)
vtkarray.SetName(prop)
# add the array as point data
mesh.point_data.add_array(vtkarray)
# set the last prop as the active scalar
mesh.point_data.set_active_scalars(props[-1])
# spit it out
fileno = data['solver_data']['count']
_fname = self.fname + '_%s_%s' % (array_name, fileno)
self._write_vtk_snapshot(mesh, dirname, _fname)
def make_binder(path):
src_path = os.path.abspath(path)
sim_paths_list = find_sim_dirs(src_path)
for path in sim_paths_list:
sim_name = os.path.split(path)[1]
make_notebook(path, sim_name)
if len(sim_paths_list) == 1 and sim_paths_list[0] == src_path:
files = os.listdir(src_path)
files = [os.path.join(src_path, f) for f in files]
mkdir(os.path.join(src_path, sim_name))
could_not_copy = []
for f in files:
try:
copy(f, os.path.join(src_path, sim_name))
except BaseException as exc:
could_not_copy.append([f, exc])
continue
os.remove(f)
if len(could_not_copy) != 0:
print("Could not copy the following files:\n")
for f in could_not_copy:
print('file: ', f[0])
print('error: ', f[1], '\n')
with open(os.path.join(src_path, 'requirements.txt'), 'w') as file:
file.write(
"ipympl\n" +
"matplotlib\n" +
"ipyvolume\n" +
"numpy\n" +
"pytools\n" +
"-e git+https://github.com/pypr/compyle#egg=compyle\n" +
"-e git+https://github.com/pypr/pysph#egg=pysph"
)
with open(os.path.join(src_path, 'README.md'), 'w') as file:
file.write(
"# Title\n" +
"[]" +
"(https://mybinder.org/v2/gh/user_name/repo_name/branch_name)" +
"\n" +
"[comment]: # (The above link is for repositories hosted " +
"on GitHub. For links corresponding to other hosting services, " +
"please visit https://mybinder.readthedocs.io)"
)
def _save_all_plots_handler(self, change):
import ipyvolume as p3
if change['new'] is True:
mkdir('all_plots')
self._widgets.play_button.disabled = True
self._widgets.delay_box.disabled = True
self._widgets.save_figure.disabled = True
self._widgets.save_all_plots.disabled = True
for array_name in self._widgets.particles.keys():
pa_widgets = self._widgets.particles[array_name]
pa_widgets.scalar.disabled = True
pa_widgets.scalar_cmap.disabled = True
pa_widgets.velocity_vectors.disabled = True
pa_widgets.vector_size.disabled = True
pa_widgets.scalar_size.disabled = True
change = {} # dummy dictionary to be used in 'self._frame.handler'
file_count = len(self.paths_list) - 1
for i in np.arange(0, file_count + 1):
self._widgets.frame.value = i
self._frame_handler(change)
p3.savefig('all_plots/frame_%s.png' % i,
width=1000,
height=1000,
fig=self.plot)
print("Saved the plots in the folder 'all_plots'" +
" in the present working directory")
self._widgets.play_button.disabled = False
self._widgets.delay_box.disabled = False
self._widgets.save_figure.disabled = False
self._widgets.save_all_plots.disabled = False
self._widgets.save_all_plots.value = False
for array_name in self._widgets.particles.keys():
pa_widgets = self._widgets.particles[array_name]
pa_widgets.scalar.disabled = True
pa_widgets.scalar_cmap.disabled = True
pa_widgets.velocity_vectors.disabled = True
pa_widgets.vector_size.disabled = True
pa_widgets.scalar_size.disabled = True
