Merge pull request #62 from flatironinstitute/59-add-handedness-flipp…

…ing-as-a-flag-to-preprocessing-pipeline 59 add handedness flipping as a flag to preprocessing pipeline
flatironinstitute · Aug 5, 2024 · bd2728a · bd2728a
2 parents c9d649b + 626b226
commit bd2728a
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Showing 5 changed files with 28 additions and 18 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -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]

diff --git a/src/cryo_challenge/_preprocessing/dataloader.py b/src/cryo_challenge/_preprocessing/dataloader.py
@@ -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")

diff --git a/src/cryo_challenge/_preprocessing/preprocessing_pipeline.py b/src/cryo_challenge/_preprocessing/preprocessing_pipeline.py
@@ -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)
+
         # align to GT
         if submission_dataset.submission_config[str(idx)]["align"] == 1:
             print("    Aligning submission to ground truth")

diff --git a/tests/data/unprocessed_dataset_2_submissions/submission_x/submission_config.json b/tests/data/unprocessed_dataset_2_submissions/submission_x/submission_config.json
@@ -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
     }
-}
+}
diff --git a/tutorials/1_tutorial_preprocessing.ipynb b/tutorials/1_tutorial_preprocessing.ipynb
@@ -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",