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add authors file
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‎.ipynb_checkpoints/Untitled-checkpoint.ipynb

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This file was deleted.

‎AUTHORS.md

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# Project Authors
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The following people have made contributions to the project (in alphabetical
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order by last name) and are considered "The pyCATHY Developers":
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* [Benjamin Mary](https://github.com/BenjMy) -University of Padua, Italy (ORCID: 0000-0002-4065-8910)
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* [Luca Peruzzo](https://github.com/Peruz) -University of Padua, Italy (ORCID: 0000-0002-4065-8910)
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‎doc/content/gettingstarted.rst

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@@ -3,9 +3,16 @@
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Getting Started
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===============
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Three steps are required to implement a working CATHY model of a specific case study (see fig. below), namely **pre-processing**, **processing**, and **post-processing**, and the following steps are necessary to create the flow model:
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1. Create the input files for the pre-processor hap
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2. Run the pre-processor hap
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3. Create the input files for the processor CATHY
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4. Perform the simulation by running the processor CATHY
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5. Run the post-processing functions to extract and view results
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.. image:: ../img/Francesca_instructions.png
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:width: 400
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:width: 700
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:alt: Getting started
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‎pyCATHY.egg-info/PKG-INFO

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@@ -29,6 +29,7 @@ License-File: LICENSE
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[![Upload Python Package](https://github.com/BenjMy/pycathy_wrapper/actions/workflows/python-publish.yml/badge.svg)](https://github.com/BenjMy/pycathy_wrapper/actions/workflows/python-publish.yml)
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[![PyPI](https://img.shields.io/pypi/v/pycathy)](https://pypi.org/project/pycathy/)
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[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/BenjMy/pycathy_wrapper/main)
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[![Test and Coverage](https://github.com/BenjMy/pycathy_wrapper/actions/workflows/coverage.yml/badge.svg)](https://github.com/BenjMy/pycathy_wrapper/actions/workflows/coverage.yml)
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## Python package for hydrogeophysical data modeling
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‎pyCATHY.egg-info/SOURCES.txt

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Original file line numberDiff line numberDiff line change
@@ -32,6 +32,7 @@ pyCATHY/importers/cathy_outputs.py
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pyCATHY/importers/cathy_plant.py
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pyCATHY/importers/sensors_measures.py
3434
pyCATHY/plotters/__init__.py
35+
pyCATHY/plotters/cathyDA_plots.py
3536
pyCATHY/plotters/cathy_plots.py
3637
pyCATHY/tests/__init__.py
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pyCATHY/tests/test_DA_ERT_Tensio_SWC.py

‎pyCATHY.egg-info/requires.txt

+2
Original file line numberDiff line numberDiff line change
@@ -13,3 +13,5 @@ natsort
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ipywidgets
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smmap
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shapely
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imageio
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nltk

‎pyCATHY/cathy_tools.py

+3
Original file line numberDiff line numberDiff line change
@@ -1193,6 +1193,9 @@ def update_dem_parameters(self, **kwargs):
11931193
# if (key +'_list') in self.dem_parameters.keys() is False:
11941194
# dem_parameters_tmp[key +'_list'] = value
11951195

1196+
1197+
if 'zratio' in kwargs:
1198+
self.dem_parameters['nstr'] = len(kwargs['zratio'])
11961199
# self.dem_parameters = self.dem_parameters | dem_parameters_tmp
11971200
# write file
11981201
header_fmt = [1, 1, 1, 1, 3, 3, 1]

‎pyCATHY/meshtools.py

+59-59
Original file line numberDiff line numberDiff line change
@@ -1040,24 +1040,24 @@ def add_markers2mesh(
10401040

10411041

10421042
# print(hapin['xllcorner'])
1043-
print(hapin['xllcorner'],hapin['yllcorner'])
1043+
# print(hapin['xllcorner'],hapin['yllcorner'])
10441044

1045-
print('x[0],y[0]')
1046-
print(x[0],y[0])
1047-
print(x[1],y[1])
1045+
# print('x[0],y[0]')
1046+
# print(x[0],y[0])
1047+
# print(x[1],y[1])
10481048

1049-
print('*'*20)
1050-
print('initial dem shape')
1051-
print(np.shape(dem))
1052-
print(dem[0][0])
1049+
# print('*'*20)
1050+
# print('initial dem shape')
1051+
# print(np.shape(dem))
1052+
# print(dem[0][0])
10531053

10541054

10551055
dem_flip = np.flipud(dem)
10561056
# dem_flip = dem
1057-
print('*'*20)
1058-
print('flip dem shape')
1059-
print(np.shape(dem_flip))
1060-
print(dem_flip[0][0])
1057+
# print('*'*20)
1058+
# print('flip dem shape')
1059+
# print(np.shape(dem_flip))
1060+
# print(dem_flip[0][0])
10611061

10621062

10631063
# Get layer top and bottom
@@ -1078,40 +1078,40 @@ def add_markers2mesh(
10781078
else:
10791079
dem_mat3d_layers = [dem_flip - zz for zz in zone3d_top-(zone3d_top-zone3d_bot)/2]
10801080

1081-
print('*'*20)
1082-
print('dem_mat3d_layers shape')
1083-
print(np.shape(dem_mat3d_layers))
1084-
print(dem_mat3d_layers[0][0])
1081+
# print('*'*20)
1082+
# print('dem_mat3d_layers shape')
1083+
# print(np.shape(dem_mat3d_layers))
1084+
# print(dem_mat3d_layers[0][0])
10851085

10861086

1087-
print('*'*20)
1088-
print('zone3d_top shape')
1089-
print(np.shape(zone3d_top))
1090-
print(zone3d_top[0][0])
1087+
# print('*'*20)
1088+
# print('zone3d_top shape')
1089+
# print(np.shape(zone3d_top))
1090+
# print(zone3d_top[0][0])
10911091

10921092

10931093

1094-
print('*'*20)
1095-
print('x shape')
1096-
print(np.shape(x))
1094+
# print('*'*20)
1095+
# print('x shape')
1096+
# print(np.shape(x))
10971097

1098-
print('*'*20)
1099-
print('y shape')
1100-
print(np.shape(y))
1098+
# print('*'*20)
1099+
# print('y shape')
1100+
# print(np.shape(y))
11011101

11021102

11031103
# Create a regular mesh from the DEM x and y coordinates and elevation
11041104
# ------------------------------------------------------------------
11051105
xgrid, ygrid = np.meshgrid(x, y)
11061106

11071107

1108-
print('*'*20)
1109-
print('xgrid shape')
1110-
print(np.shape(xgrid))
1108+
# print('*'*20)
1109+
# print('xgrid shape')
1110+
# print(np.shape(xgrid))
11111111

1112-
print('*'*20)
1113-
print('ygrid shape')
1114-
print(np.shape(ygrid))
1112+
# print('*'*20)
1113+
# print('ygrid shape')
1114+
# print(np.shape(ygrid))
11151115

11161116
# print('je suis la')
11171117
grid_coords_dem = np.array(
@@ -1122,30 +1122,30 @@ def add_markers2mesh(
11221122
).T
11231123

11241124
# print(grid_coords_dem)
1125-
print('*'*20)
1126-
print('grid_coords_dem shape')
1127-
print(np.shape(grid_coords_dem))
1125+
# print('*'*20)
1126+
# print('grid_coords_dem shape')
1127+
# print(np.shape(grid_coords_dem))
11281128

11291129

1130-
fig, ax = plt.subplots()
1131-
ax = plt.axes(projection="3d")
1130+
# fig, ax = plt.subplots()
1131+
# ax = plt.axes(projection="3d")
11321132

1133-
cmap=ax.scatter(grid_coords_dem[:,0],
1134-
grid_coords_dem[:,1],
1135-
np.ravel(zone3d_top[0]),
1136-
c='k')
1133+
# cmap=ax.scatter(grid_coords_dem[:,0],
1134+
# grid_coords_dem[:,1],
1135+
# np.ravel(zone3d_top[0]),
1136+
# c='k')
11371137

1138-
# ax.scatter(grid3d['mesh3d_nodes'][:,0],
1139-
# grid3d['mesh3d_nodes'][:,1],
1140-
# grid3d['mesh3d_nodes'][:,2],
1141-
# s=2,
1142-
# cmap = 'coolwarm')
1143-
ax.set_xlabel('Northing (m)')
1144-
ax.set_ylabel('Easting (m)')
1138+
# # ax.scatter(grid3d['mesh3d_nodes'][:,0],
1139+
# # grid3d['mesh3d_nodes'][:,1],
1140+
# # grid3d['mesh3d_nodes'][:,2],
1141+
# # s=2,
1142+
# # cmap = 'coolwarm')
1143+
# ax.set_xlabel('Northing (m)')
1144+
# ax.set_ylabel('Easting (m)')
11451145

11461146

1147-
plt.title('grid_coords_dem l0')
1148-
plt.colorbar(cmap,ax=ax)
1147+
# plt.title('grid_coords_dem l0')
1148+
# plt.colorbar(cmap,ax=ax)
11491149

11501150

11511151
# Reduce all to 1D
@@ -1160,16 +1160,16 @@ def add_markers2mesh(
11601160
xyz_layers = np.c_[grid_coords_stk_rep, dem_mat_stk, zones3d_col_stk]
11611161

11621162

1163-
fig, ax = plt.subplots()
1164-
cmap=ax.scatter(xyz_layers[:,0],
1165-
xyz_layers[:,1],
1166-
c=xyz_layers[:,2]
1167-
)
1168-
plt.colorbar(cmap,ax=ax)
1169-
plt.title('xyz_layers')
1163+
# fig, ax = plt.subplots()
1164+
# cmap=ax.scatter(xyz_layers[:,0],
1165+
# xyz_layers[:,1],
1166+
# c=xyz_layers[:,2]
1167+
# )
1168+
# plt.colorbar(cmap,ax=ax)
1169+
# plt.title('xyz_layers')
11701170

11711171

1172-
print('_plot_cellsMarkerpts')
1172+
# print('_plot_cellsMarkerpts')
11731173
# Plot to check position of points VS mesh
11741174
# ------------------------------------------------------------------
11751175
_plot_cellsMarkerpts(mesh_pv_attributes,
@@ -1178,7 +1178,7 @@ def add_markers2mesh(
11781178
project_name)
11791179

11801180
#%%
1181-
print('_find_nearest_point2DEM')
1181+
# print('_find_nearest_point2DEM')
11821182
# Assign marker to mesh and overwrite it
11831183
# ------------------------------------------------------------------
11841184
_find_nearest_point2DEM(

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