From ad4fce01506a3ea42d4b9214fe67e2bb51cd521f Mon Sep 17 00:00:00 2001 From: Garrett Wright Date: Wed, 7 Feb 2024 14:47:41 -0500 Subject: [PATCH 1/4] Add Coef doc entry --- gallery/tutorials/aspire_introduction.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gallery/tutorials/aspire_introduction.py b/gallery/tutorials/aspire_introduction.py index f87afaee2f..ff174c6563 100644 --- a/gallery/tutorials/aspire_introduction.py +++ b/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`` From a7139c36afc13ce9a0ab7e4c79112350dc1e59c8 Mon Sep 17 00:00:00 2001 From: Garrett Wright Date: Wed, 7 Feb 2024 14:48:09 -0500 Subject: [PATCH 2/4] Add CL SDP doc entry --- gallery/tutorials/aspire_introduction.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gallery/tutorials/aspire_introduction.py b/gallery/tutorials/aspire_introduction.py index ff174c6563..f1be456e65 100644 --- a/gallery/tutorials/aspire_introduction.py +++ b/gallery/tutorials/aspire_introduction.py @@ -662,7 +662,7 @@ def noise_function(x, y): # +----------------+--------------------+-----------------+----------------+---------------------+ # |CoordinateSource| whiten | | CLSymmetryCn | | # +----------------+--------------------+-----------------+----------------+---------------------+ -# | | phase_flip | | | | +# | | phase_flip | | CommonlineSDP | | # +----------------+--------------------+-----------------+----------------+---------------------+ # | |normalize_background| | | | # +----------------+--------------------+-----------------+----------------+---------------------+ From aca246f6af486b47762e071d3ad93498ba7f9a06 Mon Sep 17 00:00:00 2001 From: Garrett Wright Date: Mon, 12 Feb 2024 12:05:06 -0500 Subject: [PATCH 3/4] Add minor boosting changes to 10081 gallery --- .../experiments/experimental_abinitio_pipeline_10081.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/gallery/experiments/experimental_abinitio_pipeline_10081.py b/gallery/experiments/experimental_abinitio_pipeline_10081.py index 45a6558a89..e6e0a30c3c 100644 --- a/gallery/experiments/experimental_abinitio_pipeline_10081.py +++ b/gallery/experiments/experimental_abinitio_pipeline_10081.py @@ -42,7 +42,7 @@ 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. @@ -117,6 +117,11 @@ # ---------------------- # # 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") From 4fee1412b74a6e8daf339b7fb5c9a603aa178523 Mon Sep 17 00:00:00 2001 From: Garrett Wright Date: Thu, 15 Feb 2024 07:58:33 -0500 Subject: [PATCH 4/4] Update intro tutorial, add C2, cleanup show plots --- gallery/tutorials/aspire_introduction.py | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/gallery/tutorials/aspire_introduction.py b/gallery/tutorials/aspire_introduction.py index f1be456e65..648750ac01 100644 --- a/gallery/tutorials/aspire_introduction.py +++ b/gallery/tutorials/aspire_introduction.py @@ -597,16 +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`` @@ -658,13 +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 | | CommonlineSDP | | +# | | phase_flip | | CLSymmetryCn | | # +----------------+--------------------+-----------------+----------------+---------------------+ -# | |normalize_background| | | | +# | |normalize_background| | CommonlineSDP | | # +----------------+--------------------+-----------------+----------------+---------------------+ # | | CTFEstimator | | | | # +----------------+--------------------+-----------------+----------------+---------------------+