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Merged
merged 1 commit into from
Jul 2, 2023
Merged

@ python-loader : replace deprecated np.float with np.float64 and upd… #11

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2 changes: 1 addition & 1 deletion VERSION.txt
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
1.0.1
1.1.1
8 changes: 4 additions & 4 deletions pyMCDS.py
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Expand Up @@ -203,7 +203,7 @@ def get_concentrations(self, species_name, z_slice=None):
a plane of voxel centers in the z-axis.
Returns
-------
conc_arr : array (np.float) shape=[nx_voxels, ny_voxels, nz_voxels]
conc_arr : array (np.float64) shape=[nx_voxels, ny_voxels, nz_voxels]
Contains the concentration of the specified chemical in each voxel.
The array spatially maps to a meshgrid of the voxel centers.
"""
Expand Down Expand Up @@ -354,15 +354,15 @@ def _read_xml(self, xml_file, output_path='.'):
# while we're at it, find the mesh
coord_str = mesh_node.find('x_coordinates').text
delimiter = mesh_node.find('x_coordinates').get('delimiter')
x_coords = np.array(coord_str.split(delimiter), dtype=np.float)
x_coords = np.array(coord_str.split(delimiter), dtype=np.float64)

coord_str = mesh_node.find('y_coordinates').text
delimiter = mesh_node.find('y_coordinates').get('delimiter')
y_coords = np.array(coord_str.split(delimiter), dtype=np.float)
y_coords = np.array(coord_str.split(delimiter), dtype=np.float64)

coord_str = mesh_node.find('z_coordinates').text
delimiter = mesh_node.find('z_coordinates').get('delimiter')
z_coords = np.array(coord_str.split(delimiter), dtype=np.float)
z_coords = np.array(coord_str.split(delimiter), dtype=np.float64)

# reshape into a mesh grid
xx, yy, zz = np.meshgrid(x_coords, y_coords, z_coords)
Expand Down
4 changes: 1 addition & 3 deletions pyMCDS_timeseries.py
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Expand Up @@ -38,7 +38,7 @@ def get_times(self):

Returns
-------
time_array : ndaray (np.float) [n_timesteps,]
time_array : ndaray (np.float64) [n_timesteps,]
Contains the 'current time' at each recorded point.
'''
time_array = np.zeros(self.timeseries.shape[0])
Expand Down Expand Up @@ -93,5 +93,3 @@ def plot_cell_type_counts(self):
ax.set_ylabel('# of cells in system')
ax.legend()
plt.show()


6 changes: 3 additions & 3 deletions read_MultiCellDS_xml.py
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Expand Up @@ -40,15 +40,15 @@ def read_MultiCellDS_xml(xml_file, output_path='.'):
# while we're at it, find the mesh
coord_str = mesh_node.find('x_coordinates').text
delimiter = mesh_node.find('x_coordinates').get('delimiter')
x_coords = np.array(coord_str.split(delimiter), dtype=np.float)
x_coords = np.array(coord_str.split(delimiter), dtype=np.float64)

coord_str = mesh_node.find('y_coordinates').text
delimiter = mesh_node.find('y_coordinates').get('delimiter')
y_coords = np.array(coord_str.split(delimiter), dtype=np.float)
y_coords = np.array(coord_str.split(delimiter), dtype=np.float64)

coord_str = mesh_node.find('z_coordinates').text
delimiter = mesh_node.find('z_coordinates').get('delimiter')
z_coords = np.array(coord_str.split(delimiter), dtype=np.float)
z_coords = np.array(coord_str.split(delimiter), dtype=np.float64)

# reshape into a mesh grid
xx, yy, zz = np.meshgrid(x_coords, y_coords, z_coords)
Expand Down
6 changes: 3 additions & 3 deletions timeseries_set/read_MultiCellDS_xml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,15 +48,15 @@ def read_MultiCellDS_xml(file_name, output_dir = '.'):
# while we're at it, find the mesh
coord_str = mesh_node.find('x_coordinates').text
delimiter = mesh_node.find('x_coordinates').get('delimiter')
x_coords = np.array(coord_str.split(delimiter), dtype=np.float)
x_coords = np.array(coord_str.split(delimiter), dtype=np.float64)

coord_str = mesh_node.find('y_coordinates').text
delimiter = mesh_node.find('y_coordinates').get('delimiter')
y_coords = np.array(coord_str.split(delimiter), dtype=np.float)
y_coords = np.array(coord_str.split(delimiter), dtype=np.float64)

coord_str = mesh_node.find('z_coordinates').text
delimiter = mesh_node.find('z_coordinates').get('delimiter')
z_coords = np.array(coord_str.split(delimiter), dtype=np.float)
z_coords = np.array(coord_str.split(delimiter), dtype=np.float64)

# reshape into a mesh grid
xx, yy, zz = np.meshgrid(x_coords, y_coords, z_coords)
Expand Down