python script update

basic_scripts/python_utilities/load_data.py

@@ -47,4 +47,48 @@ def load_grids(filename):
         Ly     = 2*np.pi/kygrid[1]
         xgrid  = np.linspace(-Lx/2,Lx/2,Nx)
         ygrid  = np.linspace(-Ly/2,Ly/2,Ny)
-    return xgrid,kxgrid,ygrid,kygrid,zgrid,pgrid,jgrid
\ No newline at end of file
+    return xgrid,kxgrid,ygrid,kygrid,zgrid,pgrid,jgrid
+
+def load_group(filename,group):
+    data = {}
+    with h5py.File(filename, 'r') as file:
+        g_  = file[f"data/"+group]
+        for key in g_.keys():
+            name='data/'+group+'/'+key
+            data[key] = file.get(name)[:]
+    return data
+
+def load_params(filename):
+    with h5py.File(filename, 'r') as file:
+        nml_str = file[f"files/STDIN.00"][0]
+        nml_str = nml_str.decode('utf-8')
+        params = read_namelist(nml_str)
+    return params
+
+# Function to read all namelists from a file
+def read_namelist(nml_str):
+    Nspecies = 1
+    all_namelists = {}
+    current_namelist = None
+    nml_str = nml_str.split('\n')
+    for line in nml_str:
+        line = line.split('!')
+        line = line[0]
+        if line.startswith('&'):
+            current_namelist = line[1:].strip()
+            if current_namelist == 'SPECIES':
+                current_namelist = current_namelist + "_" + str(Nspecies)
+                Nspecies = Nspecies + 1
+            all_namelists[current_namelist] = {}
+        elif line.startswith('/'):
+            current_namelist = None
+        elif current_namelist:
+            parts = line.split('=')
+            if len(parts) == 2:
+                key = parts[0].strip()
+                value = parts[1].strip().rstrip(',').strip("'").strip()
+                if tools.is_convertible_to_float(value):
+                    all_namelists[current_namelist][key] = float(value)
+                else:
+                    all_namelists[current_namelist][key] = value
+    return all_namelists
\ No newline at end of file

basic_scripts/python_utilities/minimal_analysis.py

@@ -12,7 +12,7 @@ import numpy as np
 import sys
 import tools
 
-# Open the HDF5 file
+#------ Open the HDF5 file
 if __name__ == "__main__":
     # No command-line argument provided, use default filename
    filename = "outputs_00.h5"
@@ -29,15 +29,31 @@ else:
     print("Usage: python minimal_analysis.py [filename, int or string (opt)]")
     sys.exit(1)
 
+#------ Load data
+# load the input parameters from the STDIN.00 file stored in the h5
+params      = loader.load_params(filename)
+
+# time traces (heat and particle fluxes)
 t0D, hflux_x = loader.load_data_0D(filename,'hflux_x')
 t0D, pflux_x = loader.load_data_0D(filename,'pflux_x')
+# 3D fields (phi and first gyromoment)
 t3D, phi, tf = loader.load_data_3D_frame(filename,'phi',10000)
 t3D, Ni00,tf = loader.load_data_3D_frame(filename,'Ni00',10000)
+# grids of the simulation
 x,kx,y,ky,z,p,j  = loader.load_grids(filename)
 
+# Examples to load data in dictionaries
+# metric (gij, dBdi, Jacobian etc.)
+metric      = loader.load_group(filename,'metric')
+# another way to load the time traces all at once
+time_traces = loader.load_group(filename,'var0d')
+
+#------ Process data
+# Fourier transform into real space at constant plane
 phi = tools.zkxky_to_xy_const_z(phi,-1)
 Ni00= tools.zkxky_to_xy_const_z(Ni00,-1)
 
+#------ Plot data
 # Plot hflux_x and pflux_x against time
 fig, axes = plt.subplots(2, 2, figsize=(10, 6))
 # Plot hflux_x

basic_scripts/python_utilities/tools.py

@@ -20,4 +20,22 @@ def closest_index(array, v):
     # Find the index of the minimum difference
     closest_index = np.argmin(absolute_diff)
     
-    return closest_index
\ No newline at end of file
+    return closest_index
+
+def is_convertible_to_float(s):
+    try:
+        float(s)
+        return True
+    except ValueError:
+        return False
+
+def numpy_array_to_list(d):
+    """
+    Recursively convert NumPy arrays to lists within a dictionary.
+    """
+    for key, value in d.items():
+        if isinstance(value, np.ndarray):
+            d[key] = value.tolist()
+        elif isinstance(value, dict):
+            d[key] = numpy_array_to_list(value)
+    return d
\ No newline at end of file