added analysis

analysis/slices.py

@@ -0,0 +1,114 @@
+import numpy as np
+
+fs = 18
+fs_titles = fs -4
+
+def plot_imshow_with_reference( data_list, 
+                                reference, 
+                                titles,
+                                vmin=None,
+                                vmax=None, 
+                                cmap='viridis'):
+    """
+    Plot the imshow of a list of 2D arrays with two rows: one for the data itself,
+    one for the data compared to a reference. Each row will have a common colorbar.
+
+    Parameters:
+    - data_list: list of 2D arrays to be plotted
+    - reference: 2D array to be used as reference for comparison
+    - titles: list of titles for each subplot
+    - cmap: colormap to be used for plotting
+    """
+    import matplotlib.pyplot as plt
+
+    if titles is None:
+        titles = [None for f in data_list]
+
+    def score(data, reference):
+        return np.linalg.norm(data-reference)/np.linalg.norm(reference)
+
+    n = len(data_list)
+    fig, axes = plt.subplots(2, n, figsize=(5 * n, 10))
+
+    if vmin is None or vmax is None:
+        vmin = min(np.quantile(data,0.01) for data in data_list)
+        vmax = max(np.quantile(data,0.99) for data in data_list)
+        vmin_diff = min(np.quantile((data-reference),0.01) for data in data_list)
+        vmax_diff = max(np.quantile((data-reference),0.99) for data in data_list)
+    else:
+        vmin_diff = vmin
+        vmax_diff = vmax
+
+    # Plot the data itself
+    for i, data in enumerate(data_list):
+        im = axes[0, i].imshow(data, cmap=cmap, origin='lower', vmin=vmin, vmax=vmax)
+        axes[0, i].set_title(titles[i], fontsize=fs_titles)
+    fig.colorbar(im, ax=axes[0, :], orientation='vertical')
+
+    # Plot the data compared to the reference
+    for i, data in enumerate(data_list):
+        im = axes[1, i].imshow(data - reference, cmap=cmap, origin='lower', vmin=vmin_diff, vmax=vmax_diff)
+        axes[1, i].set_title(f'{titles[i]} - Reference', fontsize=fs_titles)
+    fig.colorbar(im, ax=axes[1, :], orientation='vertical')
+    
+    # Add the score on the plots
+    for i, data in enumerate(data_list):
+        axes[1, i].text(0.5, 0.9, f"Score: {score(data, reference):.2e}", fontsize=10, transform=axes[1, i].transAxes, color='white')
+    # plt.tight_layout()
+
+    return fig, axes
+
+
+if __name__ == "__main__":
+    from argparse import ArgumentParser
+    parser = ArgumentParser(description='Comparisons of fields slices.')
+
+    parser.add_argument('-a','--axis', type=int, default=0, help='Axis along which the slices will be taken.')
+    parser.add_argument('-i','--index', type=int, default=None, help='Index of the slice along the axis.')
+    parser.add_argument('-d', '--directory', type=str, required=True, help='Directory containing the fields files.')
+    parser.add_argument('-ref', '--reference', type=str, default=None, help='Reference field file.')
+    parser.add_argument('-f', '--filenames', type=str, nargs='+', required=True, help='Field files to be plotted.')
+    parser.add_argument('-o', '--output', type=str, default=None, help='Output plot file name.')
+    parser.add_argument('-l', '--labels', type=str, nargs='+', default=None, help='Labels for each field.')
+    parser.add_argument('-c', '--cmap', type=str, default='viridis', help='Colormap to be used for plotting.')
+    parser.add_argument('-vmin', type=float, default=None, help='Minimum value for the colorbar.')
+    parser.add_argument('-vmax', type=float, default=None, help='Maximum value for the colorbar.')
+    parser.add_argument('-t', '--title', type=str, default=None, help='Title for the plot.')
+    parser.add_argument('-log','--log_scale', action='store_true', help='Use log scale for the data.')
+
+    args = parser.parse_args()
+
+    from pysbmy.field import read_field
+
+    ref_field = read_field(args.directory+args.reference)
+    fields = [read_field(args.directory+f) for f in args.filenames]
+
+    if args.index is None:
+        index = ref_field.N0//2
+    else:
+        index=args.index
+
+    match args.axis:
+        case 0 | 'x':
+            reference = ref_field.data[index,:,:]
+            fields = [f.data[index,:,:] for f in fields]
+        case 1 | 'y':
+            reference = ref_field.data[:,index,:]
+            fields = [f.data[:,index,:] for f in fields]
+        case 2 | 'z':
+            reference = ref_field.data[:,:,index]
+            fields = [f.data[:,:,index] for f in fields]
+        case _:
+            raise ValueError(f"Wrong axis provided : {args.axis}")
+    
+    if args.log_scale:
+        reference = np.log10(2.+reference)
+        fields = [np.log10(2.+f) for f in fields]
+    
+    fig, axes = plot_imshow_with_reference(fields,reference,args.labels, vmin=args.vmin, vmax=args.vmax,cmap=args.cmap)
+    fig.suptitle(args.title)
+    
+    if args.output is not None:
+        fig.savefig(args.output)
+    else:
+        fig.savefig(args.directory+'slices.png')