Print out resolution estimate

README.md

@@ -8,10 +8,11 @@
 
 Use Fourier shell correlation to estimate the resolution of cryo-EM images and volumes
 
-Usage:
+# Usage:
 
 ```
 $ ttfsc map1.mrc map2.mrc
+Estimated resolution using 0.143 criterion: 2.36 Å
    (Y)     ^
          1 |
 0.95000000 | ⠀⠀⠀⠀⠈⠒⠢⡀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀

pyproject.toml

@@ -41,7 +41,8 @@ dependencies = [
     "ttmask",
     "matplotlib",
     "mrcfile",
-    "plotille"
+    "plotille",
+    "rich"
 ]
 
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies

src/ttfsc/cli.py

@@ -5,7 +5,7 @@
 import typer
 import torch
 from torch_fourier_shell_correlation import fsc
-
+from rich import print as rprint
 
 cli = typer.Typer(name='ttctf', no_args_is_help=True, add_completion=False)
 
@@ -14,7 +14,8 @@ def ttfsc_cli(
     map1: Annotated[Path, typer.Argument(show_default=False)],
     map2: Annotated[Path, typer.Argument(show_default=False)],
     pixel_spacing_angstroms: Annotated[Optional[float], typer.Option('--pixel-spacing-angstroms', show_default=False, help="Pixel spacing in Å/px, taken from header if not set")] = None,
-    plot_with_matplotlib: Annotated[bool, typer.Option('--plot-with-matplotlib')] = False
+    plot_with_matplotlib: Annotated[bool, typer.Option('--plot-with-matplotlib')] = False,
+    fsc_treshold: Annotated[float, typer.Option('--fsc-treshold', show_default=False, help="FSC treshold")] = 0.143
 ):
     with mrcfile.open(map1) as f:
         map1_tensor = torch.tensor(f.data)
@@ -28,6 +29,9 @@ def ttfsc_cli(
     resolution_angstrom = 1 / (bin_centers * pixel_spacing_angstroms)
     fsc_values = fsc(map1_tensor, map2_tensor)
 
+    estimated_resolution_angstrom = resolution_angstrom[(fsc_values < fsc_treshold).nonzero()[0]-1]
+    rprint(f"Estimated resolution using {fsc_treshold} criterion: {estimated_resolution_angstrom[0]:.2f} Å")
+
     if plot_with_matplotlib:
         from matplotlib import pyplot as plt
         plt.plot(resolution_angstrom, fsc_values)