Read SMC sensors observations to assimilate

The notebook illustrate how to read SMC sensors dataset to be prepare for DA

Estimated time to run the notebook = 2min

import numpy as np
from pyCATHY.DA.cathy_DA import DA
import pandas as pd
import matplotlib.pyplot as plt
from pyCATHY.DA.cathy_DA import DA, dictObs_2pd
from pyCATHY.DA.observations import read_observations, prepare_observations, make_data_cov
from pathlib import Path
import pyvista as pv

---

simuWithDA = DA(
                dirName='./DA_with_swc',
                prj_name='import_SMC',
                notebook=True,
                )

🏁 Initiate CATHY object

date_range = pd.date_range(start='2023-01-01', end='2023-01-03', freq='H')

# Create smoother soil moisture data using cumulative sum of random changes
sm_data = {f'SM{i}': np.cumsum(np.random.normal(0, 1, len(date_range))) + 25 + 10*i for i in range(1, 4)}

# Create a dataframe with smoother data
sm_smooth = pd.DataFrame(sm_data, index=date_range)

# Plot the smoother soil moisture data
sm_smooth.plot(figsize=(12, 6), marker='o')
plt.xlabel('DateTime')
plt.ylabel('Soil Moisture (%)')
plt.title('Soil Moisture Content from SMC Sensors (Smoothed Data)')
plt.legend()
plt.xticks(rotation=45)
plt.grid(True)
plt.tight_layout()
plt.show()

sm_smooth['Seconds'] = (sm_smooth.index - sm_smooth.index[0]).total_seconds()

simuWithDA.create_mesh_vtk()

SMC_XY = [5,5]
SMC_depths = [0.05,0.25,0.75] # SMC depths
# find the altitudes of the nodes at the mesh position x, y = (0.05,0.25)
_ , closest = simuWithDA.find_nearest_node(SMC_XY)

nodes_SMC = []
closestPos = []
for d in SMC_depths:
    SMC_XYZi = [5,5,closest[0][2]-d]
    nodeId, closest = simuWithDA.find_nearest_node(SMC_XYZi)
    nodes_SMC.append(nodeId)
    closestPos.append(closest)

nodes_SMC = np.hstack(nodes_SMC)
SMC_XYZ = np.vstack(closestPos)


pl = pv.Plotter(notebook=True)
mesh = pv.read(
    Path(simuWithDA.workdir) /
    simuWithDA.project_name /
    f'vtk/{simuWithDA.project_name}.vtk'
)
pl.add_mesh(mesh,
           opacity=0.7
           )
pl.add_points(SMC_XYZ,
             color='red'
             )
pl.show_grid()
pl.show()

Traceback (most recent call last):
  File "/home/runner/work/pycathy_wrapper/pycathy_wrapper/examples/DA/plot_2_prepare_SMC_obs4DA (conflicted copy 2025-05-21 091532).py", line 52, in <module>
    simuWithDA.create_mesh_vtk()
  File "/home/runner/work/pycathy_wrapper/pycathy_wrapper/pyCATHY/cathy_tools.py", line 3807, in create_mesh_vtk
    self.run_processor(IPRT1=3, verbose=verbose)
  File "/home/runner/work/pycathy_wrapper/pycathy_wrapper/pyCATHY/cathy_tools.py", line 584, in run_processor
    self.update_parm(**kwargs) # to uncomment
  File "/home/runner/work/pycathy_wrapper/pycathy_wrapper/pyCATHY/cathy_tools.py", line 1858, in update_parm
    self.update_cathyH(
  File "/home/runner/work/pycathy_wrapper/pycathy_wrapper/pyCATHY/cathy_tools.py", line 776, in update_cathyH
    self.update_veg_map()
  File "/home/runner/work/pycathy_wrapper/pycathy_wrapper/pyCATHY/cathy_tools.py", line 3353, in update_veg_map
    indice_veg, str_hd_rootmap = in_CT.read_root_map(os.path.join(
  File "/home/runner/work/pycathy_wrapper/pycathy_wrapper/pyCATHY/importers/cathy_inputs.py", line 529, in read_root_map
    with open(os.path.join(rootmapfile), "r") as f:  # open the file for reading
FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/pycathy_wrapper/pycathy_wrapper/examples/DA/./DA_with_swc/import_SMC/input/veg_map'

abs_data_err = 1e-1 # constant error does not vary with time
dict_obs = {} # initiate the dictionnary

for i in range(len(sm_smooth.columns)-1):
    for j, assimilation_time_sec in enumerate(sm_smooth['Seconds']):
        dict_obs = read_observations(
                                        dict_obs,
                                        obs_2_add=sm_smooth[sm_smooth.columns[i]].iloc[j],
                                        tA=assimilation_time_sec,
                                        mesh_nodes = nodes_SMC[i],
                                        data_type='swc',
                                        data_err=abs_data_err,
                                        colname=' m³/m³ Water Content',
                                        datetime=sm_smooth.index[j]
                                        )

data_measure_df = dictObs_2pd(dict_obs)
data_measure_df

By default, there is no correlation between sensors Therefore, the covariance matrices are diagonal with the error values on the diagonals

_,_, stacked_data_cov = make_data_cov(
                                        simuWithDA,
                                        dict_obs,
                                        list_assimilated_obs = 'swc',
                                        )
print(np.shape(stacked_data_cov))
simuWithDA.stacked_data_cov = stacked_data_cov

import pickle
with open('obs_prepared_SMC.pkl', 'wb') as fp:
    pickle.dump(dict_obs, fp)