ruff + black + fix YOGO_CLASS_ORDERING import

lfm_data_utilities/__init__.py

@@ -0,0 +1,9 @@
+YOGO_CLASS_ORDERING = [
+    "healthy",
+    "ring",
+    "trophozoite",
+    "schizont",
+    "gametocyte",
+    "wbc",
+    "misc",
+]

lfm_data_utilities/image_processing/orb_flowrate_plot.py

@@ -1,6 +1,5 @@
 import argparse
 from pathlib import Path
-import pickle
 
 import cv2
 import matplotlib.pyplot as plt

lfm_data_utilities/image_processing/xcorr_flowrate_plot.py

@@ -1,6 +1,5 @@
 import argparse
 from pathlib import Path
-import pickle
 
 import cv2
 import matplotlib.pyplot as plt

lfm_data_utilities/malaria_labelling/generate_tasks_from_list.py

@@ -26,9 +26,7 @@
 from collections import defaultdict
 from typing import List, Tuple, Dict
 
-from yogo.data import YOGO_CLASS_ORDERING
-
-
+from lfm_data_utilities import YOGO_CLASS_ORDERING
 from lfm_data_utilities.malaria_labelling.labelling_constants import IMG_SERVER_ROOT
 from lfm_data_utilities.malaria_labelling.generate_labelstudio_tasks import (
     generate_tasks_for_runset,

lfm_data_utilities/malaria_labelling/label_studio_converter/convert_yolo_to_ls.py

@@ -5,7 +5,6 @@
 Read Apache-2.0 license here https://www.apache.org/licenses/LICENSE-2.0
 """
 
-
 import os
 import sys
 import json  # better to use "imports ujson as json" for the best performance

lfm_data_utilities/malaria_labelling/label_studio_converter/create_ls_file.py

@@ -7,8 +7,7 @@
 from urllib.request import pathname2url
 from typing import Any, List, Dict, Tuple, Literal
 
-from yogo.data import YOGO_CLASS_ORDERING
-
+from lfm_data_utilities import YOGO_CLASS_ORDERING
 from lfm_data_utilities.utils import path_relative_to
 
 from lfm_data_utilities.malaria_labelling.labelling_constants import (

lfm_data_utilities/malaria_labelling/visualize_boxes.py

@@ -10,9 +10,9 @@
 from typing import Generator, Iterable, Tuple
 
 from yogo.utils.utils import bbox_colour
-from yogo.data import YOGO_CLASS_ORDERING
 from yogo.data.yogo_dataset import load_labels
 
+from lfm_data_utilities import YOGO_CLASS_ORDERING
 
 signal.signal(signal.SIGINT, signal.SIG_DFL)
 

lfm_data_utilities/model_evaluations/autofocus/filepath_dataloader.py

@@ -84,8 +84,7 @@ def __getitem__(self, index: int) -> Tuple[torch.Tensor, torch.Tensor, str]:
         return sample, target, img_path
 
 
-class InvalidDatasetDescriptionFile(Exception):
-    ...
+class InvalidDatasetDescriptionFile(Exception): ...
 
 
 @dataclass

lfm_data_utilities/model_evaluations/yogo/calculate_titration.py

@@ -24,8 +24,8 @@
     count_cells_for_formatted_preds,
 )
 from yogo.utils import format_preds
-from yogo.data import YOGO_CLASS_ORDERING
 
+from lfm_data_utilities import YOGO_CLASS_ORDERING
 from lfm_data_utilities import utils
 
 
@@ -194,9 +194,7 @@ def plot_normalized_parasitemia(points, counts, plot_dir, model_name):
         points,
         [c[1:5].sum().item() / c[:5].sum().item() for c in counts],
     )
-    ax.plot(
-        points, [initial_parasitemia / 2**i for i in range(len(titration_results))]
-    )
+    ax.plot(points, [initial_parasitemia / 2**i for i in range(len(titration_results))])
     ax.legend(["YOGO predictions", "Ground Truth"])
 
     file_name = f"normalized_{Path(model_name).with_suffix('.png')}"

lfm_data_utilities/model_evaluations/yogo/n_fold_testing/n_fold_test.py

@@ -16,13 +16,14 @@
 from yogo.model import YOGO
 from yogo.train import Trainer
 from yogo.utils import choose_device
-from yogo.data import YOGO_CLASS_ORDERING
 from yogo.data.yogo_dataset import ObjectDetectionDataset
 from yogo.data.yogo_dataloader import choose_dataloader_num_workers, collate_batch
 from yogo.data.data_transforms import DualInputId
 from yogo.data.dataset_definition_file import DatasetDefinition
 from yogo.utils.default_hyperparams import DefaultHyperparams as df
 
+from lfm_data_utilities import YOGO_CLASS_ORDERING
+
 # set seeds so we can reproduce + if we do this w/ slurm arrays,
 # each job could pick a separate fold for calculation
 torch.manual_seed(7271978)

lfm_data_utilities/model_evaluations/yogo/rank_yogo_loss.py

@@ -27,14 +27,16 @@
 from yogo.utils.utils import bbox_colour
 from yogo.utils import draw_yogo_prediction
 from yogo.data.dataset_definition_file import DatasetDefinition
-from yogo.data import YOGO_CLASS_ORDERING
 from yogo.data.yogo_dataset import (
     ObjectDetectionDataset,
     label_file_to_tensor,
     load_labels,
 )
 
 
+from lfm_data_utilities import YOGO_CLASS_ORDERING
+
+
 class YOGOPerLabelLoss(YOGOLoss):
     def forward(
         self, pred_batch: torch.Tensor, label_batch: torch.Tensor

lfm_data_utilities/model_evaluations/yogo/uncertainty_estimation/calibrate_uncertainty.py

@@ -5,7 +5,7 @@
 from scipy.optimize import curve_fit
 from pathlib import Path
 
-from yogo.data import YOGO_CLASS_ORDERING
+from lfm_data_utilities import YOGO_CLASS_ORDERING
 
 
 def sigmoid(x, a, b):

lfm_data_utilities/model_evaluations/yogo/yogo_output_analyzer/yogo_output_analyzer.py

@@ -15,7 +15,10 @@
 from dash import Dash, ctx, dcc, html, callback, Input, Output, State
 
 
-CLASS_LIST = yogo.data.YOGO_CLASS_ORDERING
+from lfm_data_utilities import YOGO_CLASS_ORDERING
+
+
+CLASS_LIST = YOGO_CLASS_ORDERING
 
 
 def set_universal_fig_settings_(fig, img_shape, prediction_shape, scale=0.8):

lfm_data_utilities/thumbnail_labelling/create_thumbnails.py

@@ -23,8 +23,9 @@
 
 
 class TasksJsonGenerationFunc(Protocol):
-    def __call__(self, image_path: Path, label_path: Path, tasks_path: Path) -> None:
-        ...
+    def __call__(
+        self, image_path: Path, label_path: Path, tasks_path: Path
+    ) -> None: ...
 
 
 def create_tasks_file_from_path_to_run(

lfm_data_utilities/thumbnail_labelling/sort_thumbnails.py

@@ -8,8 +8,7 @@
 from collections import defaultdict
 from typing import List, Dict, Tuple, DefaultDict, cast
 
-from yogo.data import YOGO_CLASS_ORDERING
-
+from lfm_data_utilities import YOGO_CLASS_ORDERING
 from lfm_data_utilities.utils import timing_context_manager
 from lfm_data_utilities.malaria_labelling.labelling_constants import CLASSES
 from lfm_data_utilities.malaria_labelling.label_studio_converter.convert_ls_to_yolo import (

lfm_data_utilities/thumbnail_labelling/tests/test_resorting.py

@@ -12,8 +12,7 @@
 
 from tqdm import tqdm
 
-from yogo.data import YOGO_CLASS_ORDERING
-
+from lfm_data_utilities import YOGO_CLASS_ORDERING
 from lfm_data_utilities.malaria_labelling.thumbnail_labelling.sort_thumbnails import (
     sort_thumbnails,
 )

lfm_data_utilities/thumbnail_labelling/thumbnail_sort_labelling.py

@@ -25,7 +25,7 @@
 
 from pathlib import Path
 
-from yogo.data import YOGO_CLASS_ORDERING
+from lfm_data_utilities import YOGO_CLASS_ORDERING
 
 from lfm_data_utilities.thumbnail_labelling.sort_thumbnails import (
     sort_thumbnails,