Doc updates 24q1

gallery/experiments/experimental_abinitio_pipeline_10081.py

@@ -41,7 +41,7 @@
 
 n_imgs = None  # Set to None for all images in starfile, can set smaller for tests.
 img_size = 32  # Downsample the images/reconstruction to a desired resolution
-n_classes = 2000  # How many class averages to compute.
+n_classes = 500  # How many class averages to compute.
 n_nbor = 100  # How many neighbors to stack
 starfile_in = "10081/data/particle_stacks/data.star"
 data_folder = "."  # This depends on the specific starfile entries.
@@ -116,6 +116,11 @@
 # ----------------------
 #
 # Using the oriented source, attempt to reconstruct a volume.
+# Since this is a Cn symmetric molecule, as indicated by
+# ``symmetry="C4"`` above, the ``avgs`` images set will be repeated
+# for each of the 3 additional rotations during the back-projection
+# step.  This boosts the effective number of images used in the
+# reconstruction from ``n_classes`` to ``4*n_classes``.
 
 logger.info("Begin Volume reconstruction")
 

gallery/tutorials/aspire_introduction.py

@@ -61,6 +61,8 @@
 #
 #    * - Component
 #      - Description
+#    * - ``Coef``
+#      - Utility class for stacks of 1D arrays.
 #    * - ``Image``
 #      - Utility class for stacks of 2D arrays.
 #    * - ``Volume``
@@ -595,16 +597,20 @@ def noise_function(x, y):
 
 # %%
 # Clean projections.
-sim.projections[:5].show()
+sim.projections[:3].show()
 
 # %%
 # Images with only CTF applied.
-sim.clean_images[:5].show()
+sim.clean_images[:3].show()
 
 # %%
-# The first five corrupted images.
-sim.images[:5].show()
+# And now the first four corrupted images.
+sim.images[:4].show(columns=2, colorbar=False)
 
+# %%
+# .. note::
+#     Above the ``show`` call has been customized as a 2 column grid
+#     with out colorbar legend.
 
 # %%
 # Real Experimental Data - ``RelionSource``
@@ -656,13 +662,13 @@ def noise_function(x, y):
 # +================+====================+=================+================+=====================+
 # |Simulation      | NoiseEstimator     | Class Averaging | CLSyncVoting   | MeanVolumeEstimator |
 # +----------------+--------------------+-----------------+----------------+---------------------+
-# |RelionSource    | downsample         | cov2d (CWF)     | CLSymmetryC3C4 |                     |
+# |RelionSource    | downsample         | cov2d (CWF)     | CLSymmetryC2   |                     |
 # +----------------+--------------------+-----------------+----------------+---------------------+
-# |CoordinateSource| whiten             |                 | CLSymmetryCn   |                     |
+# |CoordinateSource| whiten             |                 | CLSymmetryC3C4 |                     |
 # +----------------+--------------------+-----------------+----------------+---------------------+
-# |                | phase_flip         |                 |                |                     |
+# |                | phase_flip         |                 | CLSymmetryCn   |                     |
 # +----------------+--------------------+-----------------+----------------+---------------------+
-# |                |normalize_background|                 |                |                     |
+# |                |normalize_background|                 | CommonlineSDP  |                     |
 # +----------------+--------------------+-----------------+----------------+---------------------+
 # |                | CTFEstimator       |                 |                |                     |
 # +----------------+--------------------+-----------------+----------------+---------------------+