bugfix convert snapshots to density

sbmy_control/analysis/power_spectrum.py

@@ -1,7 +1,7 @@
 import numpy as np
 import os
 
-kmin = 1e-1
+nfirst_kmodes = 10
 kmax = 2e0
 Nk = 50
 AliasingCorr=False
@@ -24,12 +24,17 @@ def crop_field(field, Ncrop):
         field.L2 = field.N2*d2
 
 
-def get_power_spectrum(field, kmin=kmin, kmax=kmax, Nk=Nk, G=None):
+def get_power_spectrum(field, nfirst_kmodes=nfirst_kmodes, kmax=kmax, Nk=Nk, G=None):
     from pysbmy.power import PowerSpectrum
     from pysbmy.fft import FourierGrid
     from pysbmy.correlations import get_autocorrelation
 
     if G is None:
+        default_k_modes = PowerSpectrum(field.L0,field.L1,field.L2,int(field.N0),int(field.N1),int(field.N2),).FourierGrid.k_modes
+        if kmax is None:
+            kmax = default_k_modes[-1]
+        if kmax > default_k_modes[-1]:
+            raise ValueError(f"kmax ({kmax}) is larger than the maximum k mode available in the field ({default_k_modes[-1]}).")
         G = FourierGrid(
             field.L0,
             field.L1,
@@ -37,8 +42,8 @@ def get_power_spectrum(field, kmin=kmin, kmax=kmax, Nk=Nk, G=None):
             int(field.N0),
             int(field.N1),
             int(field.N2),
-            k_modes=np.concat([PowerSpectrum(field.L0,field.L1,field.L2,int(field.N0),int(field.N1),int(field.N2),).FourierGrid.k_modes[:10],np.logspace(
-                np.log10(kmin),
+            k_modes=np.concat([default_k_modes[:nfirst_kmodes],np.logspace(
+                np.log10(default_k_modes[nfirst_kmodes]),
                 np.log10(kmax),
                 Nk,
             )]),
@@ -51,13 +56,18 @@ def get_power_spectrum(field, kmin=kmin, kmax=kmax, Nk=Nk, G=None):
     return G, k, Pk
 
 
-def get_cross_correlations(field_A, field_B, kmin=kmin, kmax=kmax, Nk=Nk, G=None):
+def get_cross_correlations(field_A, field_B, nfirst_kmodes=nfirst_kmodes, kmax=kmax, Nk=Nk, G=None):
     from pysbmy.power import PowerSpectrum
     from pysbmy.fft import FourierGrid
     from pysbmy.correlations import get_crosscorrelation
 
 
     if G is None:
+        default_k_modes = PowerSpectrum(field_A.L0,field_A.L1,field_A.L2,int(field_A.N0),int(field_A.N1),int(field_A.N2),).FourierGrid.k_modes
+        if kmax is None:
+            kmax = default_k_modes[-1]
+        if kmax > default_k_modes[-1]:
+            raise ValueError(f"kmax ({kmax}) is larger than the maximum k mode available in the field ({default_k_modes[-1]}).")
         G = FourierGrid(
             field_A.L0,
             field_A.L1,
@@ -65,8 +75,8 @@ def get_cross_correlations(field_A, field_B, kmin=kmin, kmax=kmax, Nk=Nk, G=None
             int(field_A.N0),
             int(field_A.N1),
             int(field_A.N2),
-            k_modes=np.concat([PowerSpectrum(field_A.L0,field_A.L1,field_A.L2,int(field_A.N0),int(field_A.N1),int(field_A.N2),).FourierGrid.k_modes[:10],np.logspace(
-                np.log10(kmin),
+            k_modes=np.concat([default_k_modes[:nfirst_kmodes],np.logspace(
+                np.log10(default_k_modes[nfirst_kmodes]),
                 np.log10(kmax),
                 Nk,
             )]),
@@ -104,7 +114,7 @@ def plot_power_spectra(filenames,
                        yticks = np.linspace(0.9,1.1,11),
                        bound1=0.01,
                        bound2=0.02,
-                       kmin=kmin,
+                       nfirst_kmodes=nfirst_kmodes,
                        kmax=kmax,
                        Nk=Nk,
                        figsize=(8,4),
@@ -139,7 +149,7 @@ def plot_power_spectra(filenames,
                                                   color=colors[i],
                                                   linestyle=linestyles[i],
                                                   marker=markers[i],),
-                                   power_args=dict(kmin=kmin,
+                                   power_args=dict(nfirst_kmodes=nfirst_kmodes,
                                                    kmax=kmax,
                                                    Nk=Nk),
                                     )
@@ -178,7 +188,7 @@ def plot_cross_correlations(filenames_A,
                             yticks = np.linspace(0.99,1.001,12),
                             bound1=0.001,
                             bound2=0.002,
-                            kmin=kmin,
+                            nfirst_kmodes=nfirst_kmodes,
                             kmax=kmax,
                             Nk=Nk,
                             figsize=(8,4),
@@ -217,7 +227,7 @@ def plot_cross_correlations(filenames_A,
                                                        color=colors[i],
                                                        linestyle=linestyles[i],
                                                        marker=markers[i],),
-                                       power_args=dict(kmin=kmin,
+                                       power_args=dict(nfirst_kmodes=nfirst_kmodes,
                                                         kmax=kmax,
                                                         Nk=Nk),
                                         )   
@@ -283,8 +293,15 @@ def console_main():
     parser.add_argument('-yrp', '--ylim_power', type=float, nargs=2, default=[0.9,1.1], help='Y-axis limits.')
     parser.add_argument('-yrc', '--ylim_corr', type=float, nargs=2, default=[0.99,1.001], help='Y-axis limits.')
     parser.add_argument('--crop', type=int, default=None, help='Remove the outter N pixels of the fields.')
+    parser.add_argument('--nfirst_kmodes', type=float, default=10, help='First k modes from all available k modes to be used in the power spectrum before the geomspace part.')
+    parser.add_argument('--kmax', type=float, default=None, help='Maximum k value for the power spectrum geomspace part. If None, it will be set to the maximum k mode available in the field.')
+    parser.add_argument('--Nk', type=int, default=50, help='Number of k values for the power spectrum geomspace part.')
 
     args = parser.parse_args()
+    
+    nfirst_kmodes = args.nfirst_kmodes
+    kmax = args.kmax
+    Nk = args.Nk
 
     if not args.power_spectrum and not args.cross_correlation:
         print('You must choose between power_spectrum and cross_correlation.')
@@ -298,7 +315,7 @@ def console_main():
         from pysbmy.field import read_field
         F_ref = read_field(args.directory+args.reference)
         crop_field(F_ref, args.crop)
-        G, _, Pk_ref = get_power_spectrum(F_ref, kmin=kmin, kmax=kmax, Nk=Nk)
+        G, _, Pk_ref = get_power_spectrum(F_ref, nfirst_kmodes=nfirst_kmodes, kmax=kmax, Nk=Nk)
     else:
         Pk_ref = None
         G = None
@@ -325,7 +342,7 @@ def console_main():
                            yticks = yticks_power,
                            bound1=0.01,
                            bound2=0.02,
-                           kmin=kmin,
+                           nfirst_kmodes=nfirst_kmodes,
                            kmax=kmax,
                            Nk=Nk,
                            ax=axes[0],
@@ -344,7 +361,7 @@ def console_main():
                                 yticks = yticks_corr,
                                 bound1=0.001,
                                 bound2=0.002,
-                                kmin=kmin,
+                                nfirst_kmodes=nfirst_kmodes,
                                 kmax=kmax,
                                 Nk=Nk,
                                 ax=axes[1],
@@ -371,7 +388,7 @@ def console_main():
                                     yticks = yticks_power,
                                      bound1=0.01,
                                      bound2=0.02,
-                                     kmin=kmin,
+                                     nfirst_kmodes=nfirst_kmodes,
                                      kmax=kmax,
                                      Nk=Nk,
                                     Ncrop=args.crop,
@@ -392,7 +409,7 @@ def console_main():
                                         yticks = yticks_corr,
                                           bound1=0.001,
                                           bound2=0.002,
-                                          kmin=kmin,
+                                          nfirst_kmodes=nfirst_kmodes,
                                           kmax=kmax,
                                           Nk=Nk,
                                         Ncrop=args.crop,

sbmy_control/monofonic.py

@@ -32,7 +32,7 @@ def main_monofonic(parsed_args):
         print_message("Running monofonic in slurm mode.", 1, "monofonic", verbose=parsed_args.verbose)
         slurm_dict=parse_arguments_slurm(parsed_args)
         main_dict=parse_arguments_main(parsed_args)
-        slurm_script = slurm_dict["scripts"]+"monofonic.sh"
+        slurm_script = slurm_dict["scripts"]+f"monofonic_{main_dict['simname']}.sh"
 
         if not isfile(slurm_script) or parsed_args.force:
             print_message(f"SLURM script {slurm_script} does not exist (or forced). Creating it.", 2, "monofonic", verbose=parsed_args.verbose)

sbmy_control/parameters_monofonic.py

@@ -95,8 +95,6 @@ def get_config_from_dict(monofonic_dict):
             "Omega_L": monofonic_dict["Omega_q"],
             "H0": monofonic_dict["h"]*100.,
             "n_s": monofonic_dict["n_s"],
-            "sigma_8": monofonic_dict["sigma8"],
-            "A_s": monofonic_dict["A_s"],
             "Tcmb": monofonic_dict["Tcmb"],
             "k_p": monofonic_dict["k_p"],
             "N_ur": monofonic_dict["N_ur"],
@@ -110,7 +108,14 @@ def get_config_from_dict(monofonic_dict):
             "transfer": "CLASS",
             "ztarget": 2.5,
             "ZeroRadiation": False
-        } 
+        }
+
+        if "A_s" in monofonic_dict.keys() and monofonic_dict["A_s"] is not None:
+            config["cosmology"]["A_s"] = monofonic_dict["A_s"]
+        elif "sigma8" in monofonic_dict.keys() and monofonic_dict["sigma8"] is not None:
+            config["cosmology"]["sigma8"] = monofonic_dict["sigma8"]
+        else:
+            raise KeyError("Either A_s or sigma8 must be provided in the cosmology parameters.")
 
     config["random"] = {
         "generator": "NGENIC",

sbmy_control/scripts/convert_snapshot_to_density.py

@@ -1,9 +1,7 @@
-from pysbmy.density import get_density_pm_snapshot
-from pysbmy.snapshot import read_snapshot
 import argparse
 
 
-def convert_snapshot_to_density(snapshot_path, output_path, N=None, corner=(0.0, 0.0, 0.0)):
+def convert_snapshot_to_density(snapshot_path, output_path, N=None, corner=(0.0, 0.0, 0.0), time=1.0):
     """
     Convert a snapshot to a density field.
 
@@ -18,6 +16,9 @@ def convert_snapshot_to_density(snapshot_path, output_path, N=None, corner=(0.0,
     corner : tuple of float
         Corner of the box (x, y, z).
     """
+    from pysbmy.density import get_density_pm_snapshot
+    from pysbmy.snapshot import read_snapshot
+
     # Read the snapshot
     print("Reading snapshot...")
     snap = read_snapshot(snapshot_path)
@@ -28,12 +29,86 @@ def convert_snapshot_to_density(snapshot_path, output_path, N=None, corner=(0.0,
     # Calculate density
     print("Calculating density...")
     F = get_density_pm_snapshot(snap, N, N, N, corner[0], corner[1], corner[2])
+    F.time = time  # Set the time for the field
 
     # Write density to file
     print("Writing density...")
     F.write(output_path)
     print("Density written to", output_path)
     print("Done.")
+    
+
+def convert_snapshots_to_density(snapshot_base_path, output_path, N=None, corner=(0.0, 0.0, 0.0), time=1.0):
+    """
+    Convert multiple snapshots to density fields.
+
+    Parameters
+    ----------
+    snapshot_base_path : str
+        Base path for the snapshot files.
+    output_path : str
+        Path to the output density file.
+    N : int
+        Size of the density field grid (N x N x N).
+    corner : tuple of float
+        Corner of the box (x, y, z).
+    """
+    from pysbmy.density import get_density_pm, density_to_delta
+    from pysbmy.snapshot import read_snapshot
+    from pysbmy.field import Field
+    import numpy as np
+    
+    # Get all snapshot files with path "snapshot_base_path*"
+    import glob
+    
+    snapshot_files = glob.glob(snapshot_base_path + "*")
+    if not snapshot_files:
+        raise FileNotFoundError(f"No snapshot files found at {snapshot_base_path}")
+    
+    A = None
+    L0 = L1 = L2 = None
+    d0 = d1 = d2 = None
+    
+    for snapshot_path in snapshot_files:
+        # Read the snapshot
+        print(f"Reading snapshot {snapshot_path}...")
+        snap = read_snapshot(snapshot_path)
+        
+        if N is None:
+            N = snap.Np0
+        
+        if L0 is None:
+            # Get the grid parameters from the snapshot
+            L0 = snap.L0
+            L1 = snap.L1
+            L2 = snap.L2
+            d0 = L0 / N
+            d1 = L1 / N
+            d2 = L2 / N
+        else:
+            # Ensure the grid parameters match the first snapshot
+            if not (snap.L0 == L0 and snap.L1 == L1 and snap.L2 == L2):
+                raise ValueError(f"All snapshots must have the same grid parameters. Got {snap.L0}, {snap.L1}, {snap.L2} but expected {L0}, {L1}, {L2}.")
+        
+        if A is None:
+            # Initialize the density field
+            A = np.zeros((N, N, N), dtype=np.float32)
+
+        # Calculate density
+        print("Calculating density for this snapshot...")
+        A = get_density_pm(snap.pos, A, d0=d0, d1=d1, d2=d2)
+    
+    # Convert density to delta field
+    print("Converting density to delta field...")
+    A = density_to_delta(A)
+    
+    # Create a Field object
+    F = Field(L0=L0,L1=L1,L2=L2,corner0=corner[0],corner1=corner[1],corner2=corner[2],rank=1,N0=N,N1=N,N2=N,time=time,data=A)
+    # Write density to file
+    print("Writing density...")
+    F.write(output_path)
+    print("Density written to", output_path)
+    print("Done.")
 
 
 def console_main():
@@ -70,13 +145,23 @@ def console_main():
 
     args = parser.parse_args()
 
-    convert_snapshot_to_density(
-        snapshot_path=args.snapshot,
-        output_path=args.output,
-        N=args.N,
-        corner=args.corner,
-    )
+    if args.snapshot.endswith("h5") or args.snapshot.endswith("hdf5") or args.snapshot.endswith("gadget3"):
+        # If the snapshot is a single file, convert it to density
+        convert_snapshot_to_density(
+            snapshot_path=args.snapshot,
+            output_path=args.output,
+            N=args.N,
+            corner=args.corner,
+        )
+    else:
+        # If the snapshot is a base path, convert all snapshots to density
+        convert_snapshots_to_density(
+            snapshot_base_path=args.snapshot,
+            output_path=args.output,
+            N=args.N,
+            corner=args.corner,
+        )
 
 
 if __name__ == "__main__":
-    console_main()
+    console_main()

sbmy_control/simbelmyne.py

@@ -16,7 +16,7 @@ def main_simbelmyne(parsed_args):
 
         if isfile(log_file): # Remove the preexisting log file to allow for the progress_bar to be run normally
             from os import remove
-            oremove(log_file)
+            remove(log_file)
 
         command_args = ["simbelmyne", paramfile, log_file]