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feat: Add constrained search tutorial #37

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feat: Add constrained search tutorial #37

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391ad93
feat: Add constrained search tutorial
jdickerson95 May 8, 2025
baefee5
Merge branch 'jd_fourier_slice_fix' into constrained_tutorial
jdickerson95 May 8, 2025
c13c86f
Merge branch 'main' into constrained_tutorial
mgiammar May 19, 2025
89944e9
feat: begin work porting notebook into MkDocs website
mgiammar May 21, 2025
0be3d4f
feat: simplify rotation axis script
mgiammar May 21, 2025
7139792
feat: simplify center vector script
mgiammar May 21, 2025
9898915
feat: more work on porting over the constrained tutorial (unfinished)
mgiammar May 21, 2025
6418cb7
Clean up sequential processing script
jdickerson95 May 25, 2025
6cd000a
Updated notebook with fixed configs and updated Zenodo
jdickerson95 May 26, 2025
6df97f3
forgot to save with new Zenodo link
jdickerson95 May 26, 2025
f6fa5b9
fix: no multiple centre offsets
jdickerson95 Jun 10, 2025
d528726
Update constrained_search_example_config.yaml
jdickerson95 Jun 16, 2025
a792e87
fix: Update tutorial for new simulation
jdickerson95 Jun 23, 2025
629c453
update zenodo link
jdickerson95 Jun 23, 2025
0a5b183
correct typos
jdickerson95 Jun 30, 2025
ebf00af
merge main
jdickerson95 Jul 3, 2025
d365cd4
update zenodo link for new refine. Update programs config example
jdickerson95 Jul 3, 2025
f1cfc32
fix: make sure b_env on same device as ctf
jdickerson95 Jul 13, 2025
bfa246c
Merge branch 'pr-63' into constrained_tutorial
jdickerson95 Jul 14, 2025
790eb29
Update tutorial for ttsim3d and Nan error
jdickerson95 Jul 25, 2025
efd68b7
Improve constrained and add intro tutorial
jdickerson95 Aug 23, 2025
07a8087
Merge branch 'docs_main' into constrained_tutorial
mgiammar Aug 25, 2025
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10 changes: 10 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -117,6 +117,16 @@ ENV/
# Temporary files
*.tmp

#########################################
### Paths/dirs specific to Leopard-EM ###
#########################################

# Downloaded data for example notebooks
docs/examples/constrained_search_tutorial/configs
docs/examples/constrained_search_tutorial/maps
docs/examples/constrained_search_tutorial/mgraphs
docs/examples/constrained_search_tutorial/models
docs/examples/constrained_search_tutorial/results

small_image_test_data/
medium_image_test_data/
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3 changes: 2 additions & 1 deletion .pre-commit-config.yaml
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Expand Up @@ -20,9 +20,10 @@ repos:
rev: v1.24.6
hooks:
- id: typos
exclude: ".*\\.ipynb$" # exclude Jupyter notebooks because of metadata
args: # omitting --write-changes
- "--force-exclude"
# - "--config=_typos.toml"
- "--config=_typos.toml"

- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.7.2
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2 changes: 1 addition & 1 deletion _typos.toml
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@@ -1,2 +1,2 @@
[default.extend-words]
BA = "BA"
BA = "BA"
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