FRC and FSC cutoff=None option

gallery/tutorials/tutorials/image_class.py

@@ -14,7 +14,7 @@
 
 file_path = os.path.join(os.path.dirname(os.getcwd()), "data", "monuments.npy")
 img_data = np.load(file_path)
-img_data.shape, img_data.dtype
+print(img_data.shape, img_data.dtype)
 
 # %%
 # Create an Image Instance

src/aspire/image/image.py

@@ -571,7 +571,7 @@ def show(self, columns=5, figsize=(20, 10), colorbar=True):
 
             plt.show()
 
-    def frc(self, other, cutoff, pixel_size=None, method="fft", plot=False):
+    def frc(self, other, cutoff=None, pixel_size=None, method="fft", plot=False):
         r"""
         Compute the Fourier ring correlation between two images.
 
@@ -586,6 +586,9 @@ def frc(self, other, cutoff, pixel_size=None, method="fft", plot=False):
 
         :param other: `Image` instance to compare.
         :param cutoff: Cutoff value, traditionally `.143`.
+            Default `None` implies `cutoff=1` and excludes
+            plotting cutoff line.
+
         :param pixel_size: Pixel size in angstrom.  Default `None`
             implies unit in pixels, equivalent to pixel_size=1.
         :param method: Selects either 'fft' (on cartesian grid),

src/aspire/utils/resolution_estimation.py

@@ -2,6 +2,7 @@
 This module contains code for estimating resolution achieved by reconstructions.
 """
 import logging
+import warnings
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -44,7 +45,7 @@ def __init__(self, a, b, pixel_size=None, method="fft"):
                     Default `None` implies "pixel" units.
                 :param method: Selects either 'fft' (on Cartesian grid),
                     or 'nufft' (on polar grid). Defaults to 'fft'.
-        7"""
+        """
 
         # Sanity checks
         if not hasattr(self, "dim"):
@@ -250,7 +251,11 @@ def analyze_correlations(self, cutoff):
         Convert from the Fourier correlations to frequencies and resolution.
 
         :param cutoff: Cutoff value, traditionally `.143`.
+            Note `cutoff=None` evaluates as `cutoff=1`.
         """
+        # Handle optional cutoff plotting.
+        if cutoff is None:
+            cutoff = 1
 
         cutoff = float(cutoff)
         if not (0 <= cutoff <= 1):
@@ -271,8 +276,12 @@ def analyze_correlations(self, cutoff):
         # Convert indices to frequency (as 1/angstrom)
         frequencies = self._freq(c_ind)
 
-        # Convert to resolution in angstrom, smaller is higher frequency.
-        self._resolutions = 1 / frequencies
+        with warnings.catch_warnings():
+            # When using high cutoff (eg. 1) it is possible `frequencies`
+            # contains 0; capture and ignore that division warning.
+            warnings.filterwarnings("ignore", r".*divide by zero.*")
+            # Convert to resolution in angstrom, smaller is higher frequency.
+            self._resolutions = 1 / frequencies
 
         return self._resolutions
 
@@ -289,17 +298,25 @@ def _freq(self, k):
         # Similar to wavenumbers.  Larger is higher frequency.
         return k / (self.L * self.pixel_size)
 
-    def plot(self, cutoff, save_to_file=False, labels=None):
+    def plot(self, cutoff=None, save_to_file=False, labels=None):
         """
         Generates a Fourier correlation plot.
 
         :param cutoff: Cutoff value, traditionally `.143`.
+            Default `None` implies `cutoff=1` and excludes
+            plotting cutoff line.
         :param save_to_file: Optionally, save plot to file.
             Defaults False, enabled by providing a string filename.
             User is responsible for providing reasonable filename.
             See `https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.savefig.html`.
         """
-        cutoff = float(cutoff)
+
+        # Handle optional cutoff plotting.
+        _plot_cutoff = True
+        if cutoff is None:
+            cutoff = 1
+            _plot_cutoff = False
+
         if not (0 <= cutoff <= 1):
             raise ValueError("Supplied correlation `cutoff` not in [0,1], {cutoff}")
 
@@ -344,17 +361,20 @@ def plot(self, cutoff, save_to_file=False, labels=None):
                     _label = labels[i]
             plt.plot(freqs_units, line, label=_label)
 
-        # Display cutoff
-        plt.axhline(y=cutoff, color="r", linestyle="--", label=f"cutoff={cutoff}")
         estimated_resolution = self.analyze_correlations(cutoff)[0]
 
-        # Display resolution
-        plt.axvline(
-            x=estimated_resolution,
-            color="b",
-            linestyle=":",
-            label=f"Resolution={estimated_resolution:.3f}",
-        )
+        # Display cutoff
+        if _plot_cutoff:
+            plt.axhline(y=cutoff, color="r", linestyle="--", label=f"cutoff={cutoff}")
+
+            # Display resolution
+            plt.axvline(
+                x=estimated_resolution,
+                color="b",
+                linestyle=":",
+                label=f"Resolution={estimated_resolution:.3f}",
+            )
+
         # x-axis decreasing
         plt.gca().invert_xaxis()
         plt.legend(title=f"Method: {self.method}")

src/aspire/volume/volume.py

@@ -549,7 +549,7 @@ def load(cls, filename, permissive=True, dtype=None, symmetry_group=None):
 
         return cls(loaded_data, symmetry_group=symmetry_group, dtype=dtype)
 
-    def fsc(self, other, cutoff, pixel_size=None, method="fft", plot=False):
+    def fsc(self, other, cutoff=None, pixel_size=None, method="fft", plot=False):
         r"""
         Compute the Fourier shell correlation between two volumes.
 
@@ -564,6 +564,8 @@ def fsc(self, other, cutoff, pixel_size=None, method="fft", plot=False):
 
         :param other: `Volume` instance to compare.
         :param cutoff: Cutoff value, traditionally `.143`.
+            Default `None` implies `cutoff=1` and excludes
+            plotting cutoff line.
         :param pixel_size: Pixel size in angstrom.  Default `None`
             implies unit in pixels, equivalent to pixel_size=1.
         :param method: Selects either 'fft' (on cartesian grid),

tests/test_fourier_correlation.py

@@ -145,9 +145,10 @@ def test_frc_img_plot(image_fixture):
         _ = img_a.frc(img_n, pixel_size=1, cutoff=0.143, plot=True)
 
     # Plot to file
+    # Also tests `cutoff=None`
     with tempfile.TemporaryDirectory() as tmp_input_dir:
         file_path = os.path.join(tmp_input_dir, "img_frc_curve.png")
-        img_a.frc(img_n, pixel_size=1, cutoff=0.143, plot=file_path)
+        img_a.frc(img_n, pixel_size=1, cutoff=None, plot=file_path)
         assert os.path.exists(file_path)
 
 
@@ -204,9 +205,10 @@ def test_fsc_vol_plot(volume_fixture):
         _ = vol_a.fsc(vol_b, pixel_size=1, cutoff=0.5, plot=True)
 
     # Plot to file
+    # Also tests `cutoff=None`
     with tempfile.TemporaryDirectory() as tmp_input_dir:
-        file_path = os.path.join(tmp_input_dir, "img_fsc_curve.png")
-        vol_a.fsc(vol_b, pixel_size=1, cutoff=0.143, plot=file_path)
+        file_path = os.path.join(tmp_input_dir, "vol_fsc_curve.png")
+        vol_a.fsc(vol_b, pixel_size=1, cutoff=None, plot=file_path)
         assert os.path.exists(file_path)
 
 

tests/test_utils.py

@@ -395,7 +395,7 @@ def matplotlib_no_gui():
 
     # Save and restore current warnings list.
     with warnings.catch_warnings():
-        warnings.filterwarnings("ignore", "Matplotlib is currently using agg")
+        warnings.filterwarnings("ignore", r"Matplotlib is currently using agg.*")
 
         yield
 

tox.ini

@@ -72,6 +72,7 @@ per-file-ignores =
  gallery/tutorials/pipeline_demo.py: T201
  gallery/tutorials/turorials/data_downloader.py: E402
  gallery/tutorials/tutorials/ctf.py: T201, E402
+ gallery/tutorials/tutorials/image_class.py: T201
  gallery/tutorials/tutorials/micrograph_source.py: T201, E402
  gallery/tutorials/tutorials/weighted_volume_estimation.py: T201, E402
  # Ignore Sphinx gallery builds