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59 add handedness flipping as a flag to preprocessing pipeline #62

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merged 7 commits into from
Aug 5, 2024
Merged

59 add handedness flipping as a flag to preprocessing pipeline #62

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6f3fd9d
add flip to preprocessing
Aug 2, 2024
f82d373
Update pyproject.toml
DSilva27 Aug 5, 2024
9d8aa51
Update pyproject.toml
DSilva27 Aug 5, 2024
384eebf
Update pyproject.toml
DSilva27 Aug 5, 2024
bc341a8
update pyproject toml
Aug 5, 2024
531df87
Merge branch 'dev' into 59-add-handedness-flipping-as-a-flag-to-prepr…
Aug 5, 2024
626b226
update tutorial with flip flag
Aug 5, 2024
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32 changes: 16 additions & 16 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -38,29 +38,29 @@ classifiers = [
"Programming Language :: Python :: Implementation :: PyPy",
]
dependencies = [
"torch<=2.3.1",
"numpy<=2.0.0",
"natsort<=8.4.0",
"pandas<=2.2.2",
"dataclasses_json<=0.6.7",
"mrcfile<=1.5.0",
"scipy<=1.13.1",
"cvxpy<=1.5.2",
"POT<=0.9.3",
"aspire<=0.12.2",
"jupyter<=1.0.0",
"osfclient<=0.0.5",
"seaborn<=0.13.2",
"ipyfilechooser<=0.6.0",
"torch",
"numpy",
"natsort",
"pandas",
"dataclasses_json",
"mrcfile",
"scipy",
"cvxpy",
"POT",
"aspire",
"jupyter",
"osfclient",
"seaborn",
"ipyfilechooser",
"omegaconf"
]

[project.optional-dependencies]
dev = [
"pytest<=8.2.2",
"pytest",
"mypy",
"pre-commit",
"ruff",
"omegaconf<=2.3.0"
]

[project.urls]
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2 changes: 2 additions & 0 deletions src/cryo_challenge/_preprocessing/dataloader.py
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Expand Up @@ -65,6 +65,8 @@ def validate_submission_config(self):
raise ValueError(f"Pixel size not found for submission {key}")
if "align" not in value.keys():
raise ValueError(f"Align not found for submission {key}")
if "flip" not in value.keys():
raise ValueError(f"Flip not found for submission {key}")

if not os.path.exists(value["path"]):
raise ValueError(f"Path {value['path']} does not exist")
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5 changes: 5 additions & 0 deletions src/cryo_challenge/_preprocessing/preprocessing_pipeline.py
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Expand Up @@ -107,6 +107,11 @@ def preprocess_submissions(submission_dataset, config):
print(" Centering submission")
volumes = center_submission(volumes, pixel_size=pixel_size_gt)

# flip handedness
if submission_dataset.submission_config[str(idx)]["flip"] == 1:
print(" Flipping handedness of submission")
volumes = volumes.flip(-1)
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in the docs (notebook?) you can explain what axis (the last ) that it flips over


# align to GT
if submission_dataset.submission_config[str(idx)]["align"] == 1:
print(" Aligning submission to ground truth")
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5 changes: 3 additions & 2 deletions tests/data/unprocessed_dataset_2_submissions/submission_x/submission_config.json
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Expand Up @@ -11,6 +11,7 @@
"align": 1,
"box_size": 244,
"pixel_size": 2.146,
"path": "tests/data/unprocessed_dataset_2_submissions/submission_x"
"path": "tests/data/unprocessed_dataset_2_submissions/submission_x",
"flip": 1
}
}
}
2 changes: 2 additions & 0 deletions tutorials/1_tutorial_preprocessing.ipynb
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Expand Up @@ -136,13 +136,15 @@
" 0: {\n",
" \"name\": \"submission1\",\n",
" \"align\": 0,\n",
" \"flip\": 0,\n",
" \"box_size\": 144,\n",
" \"pixel_size\": 1.073 * 2,\n",
" \"path\": submission1_path.selected_path,\n",
" },\n",
" 1: {\n",
" \"name\": \"submission2\",\n",
" \"align\": 1,\n",
" \"flip\": 1,\n",
" \"box_size\": 288,\n",
" \"pixel_size\": 1.073,\n",
" \"path\": submission2_path.selected_path,\n",
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