review updates

Author: garrettwrong

gallery/tutorials/tutorials/micrograph_source.py

@@ -17,7 +17,7 @@
 # %%
 # Overview
 # --------
-# ``MicrographSource`` is an abstract class which provides access two
+# ``MicrographSource`` is an abstract class which provides access to
 # three distinct subclasses.  The first two are
 # ``ArrayMicrographSource`` and ``DiskMicrographSource`` which provide
 # access to array and disk backed micrograph data respectively.
@@ -154,7 +154,7 @@
 # particles.
 
 n_particles_per_micrograph = 10
-n_micrographs = 4
+n_micrographs = 3
 
 src = MicrographSimulation(
     vol,
@@ -213,7 +213,7 @@
     noise_adder=noise,
     particles_per_micrograph=n_particles_per_micrograph,
     micrograph_size=1024,
-    micrograph_count=4,
+    micrograph_count=n_micrographs,
     ctf_filters=ctfs,
     seed=1234,
 )

src/aspire/source/image.py

@@ -1000,7 +1000,7 @@ def save(
             Note, `batch_size=1` implies single MRC extension `.mrc`,
             while `batch_size>=1` implies stack MRC extension `.mrcs`.
         :param save_mode: Whether to save all images in a `single` or multiple files in batch size.
-            Default is multiple, supple `'single'` for single mode.
+            Default is multiple, supply `'single'` for single mode.
         :param overwrite: Option to overwrite the output MRC files.
         :return: A dictionary containing "starfile"--the path to the saved starfile-- and "mrcs", a
             list of the saved particle stack MRC filenames.

src/aspire/source/micrograph.py

@@ -293,15 +293,15 @@ def __init__(
         :param particles_per_micrograph: The amount of particles generated for each micrograph. Defaults to 10.
         :param particle_amplitudes: Optional, amplitudes to pass to `Simulation`.
              Default `None` uses `Simulation` defaults.
-             When provided must be array with size `particles_per_micrograph * particles_per_micrograph`.
+             When provided must be array with size `particles_per_micrograph * micrograph_count`.
         :param projection_angles: Optional, projection rotation angles to pass to `Simulation`.
              Default `None` uses `Simulation` defaults.
-             When provided must have shape `(particles_per_micrograph * particles_per_micrograph, 3)`.
+             When provided must have shape `(particles_per_micrograph * micrograph_count, 3)`.
 
         :param seed: Random seed.
         :param noise_adder: Append instance of NoiseAdder to generation pipeline.
         :param ctf_filters: Optional list of `Filter` objects to apply to particles.
-            This list should be 1, n_micrographs, or particles_per_micrograph * particles_per_micrograph.
+            This list should be 1, n_micrographs, or particles_per_micrograph * micrograph_count.
             These will apply filters to all particles, per-micrograph, or per-particle respectively.
             Default `None` will not apply any additional filters.
         :param boundary: Set boundaries for particle centers, positive values move the boundary inward from the edge of the micrograph. Defaults to half of the particle size (particle_box_size // 2).
@@ -331,7 +331,7 @@ def __init__(
 
         if self.particle_box_size > micrograph_size:
             raise ValueError(
-                "The micrograph size must be larger or equal to the simulation's image size."
+                "The micrograph size must be larger or equal to the `particle_box_size`."
             )
 
         if particle_amplitudes is not None:
@@ -340,7 +340,7 @@ def __init__(
                 and len(particle_amplitudes) != self.total_particle_count
             ):
                 raise RuntimeError(
-                    f"`len(particle_amplitudes)` must be an `int` or length {self.total_particle_count}."
+                    f"`particle_amplitudes` must be an `int` or length {self.total_particle_count}."
                 )
         self.particle_amplitudes = particle_amplitudes
 

tests/test_micrograph_simulation.py

@@ -121,7 +121,7 @@ def test_micrograph_raises_error_image_size(vol_fixture):
         )
     assert (
         str(e_info.value)
-        == "The micrograph size must be larger or equal to the simulation's image size."
+        == "The micrograph size must be larger or equal to the `particle_box_size`."
     )
 
 
@@ -306,7 +306,7 @@ def test_bad_amplitudes(vol_fixture):
     """
     Test incorrect `particle_amplitudes` argument raises.
     """
-    with pytest.raises(RuntimeError, match=r".*len\(particle_amplitudes\).*"):
+    with pytest.raises(RuntimeError, match=r".*particle_amplitudes.*"):
         _ = MicrographSimulation(
             volume=vol_fixture,
             particles_per_micrograph=1,