| Utilities API | |
| ============= | |
| Documentation for various utilities from all modules. | |
| Logging Utils | |
| ------------- | |
| .. autoapiclass:: pathml.PathMLLogger | |
| Core Utils | |
| ---------- | |
| .. autoapifunction:: pathml.core.utils.readtupleh5 | |
| .. autoapifunction:: pathml.core.utils.writedataframeh5 | |
| .. autoapifunction:: pathml.core.utils.writedicth5 | |
| .. autoapifunction:: pathml.core.utils.writestringh5 | |
| .. autoapifunction:: pathml.core.utils.writetupleh5 | |
| .. autoapifunction:: pathml.core.utils.readcounts | |
| .. autoapifunction:: pathml.core.utils.writecounts | |
| Graph Utils | |
| -------------- | |
| .. autoapifunction:: pathml.graph.utils.Graph | |
| .. autoapifunction:: pathml.graph.utils.HACTPairData | |
| .. autoapifunction:: pathml.graph.utils.get_full_instance_map | |
| .. autoapifunction:: pathml.graph.utils.build_assignment_matrix | |
| .. autoapifunction:: pathml.graph.utils.two_hop | |
| .. autoapifunction:: pathml.graph.utils.two_hop_no_sparse | |
| Datasets Utils | |
| -------------- | |
| .. autoapiclass:: pathml.datasets.utils.DeepPatchFeatureExtractor | |
| .. autoapifunction:: pathml.datasets.utils.pannuke_multiclass_mask_to_nucleus_mask | |
| .. autoapifunction:: pathml.datasets.utils._remove_modules | |
| ML Utils | |
| -------- | |
| .. autoapifunction:: pathml.ml.utils.center_crop_im_batch | |
| .. autoapifunction:: pathml.ml.utils.dice_loss | |
| .. autoapifunction:: pathml.ml.utils.dice_score | |
| .. autoapifunction:: pathml.ml.utils.get_sobel_kernels | |
| .. autoapifunction:: pathml.ml.utils.wrap_transform_multichannel | |
| .. autoapifunction:: pathml.ml.utils.scatter_sum | |
| .. autoapifunction:: pathml.ml.utils.broadcast | |
| .. autoapifunction:: pathml.ml.utils.get_degree_histogram | |
| .. autoapifunction:: pathml.ml.utils.get_class_weights | |
| Miscellaneous Utils | |
| ------------------- | |
| .. autoapifunction:: pathml.utils.upsample_array | |
| .. autoapifunction:: pathml.utils.pil_to_rgb | |
| .. autoapifunction:: pathml.utils.segmentation_lines | |
| .. autoapifunction:: pathml.utils.plot_mask | |
| .. autoapifunction:: pathml.utils.contour_centroid | |
| .. autoapifunction:: pathml.utils.sort_points_clockwise | |
| .. autoapifunction:: pathml.utils.pad_or_crop | |
| .. autoapifunction:: pathml.utils.RGB_to_HSI | |
| .. autoapifunction:: pathml.utils.RGB_to_OD | |
| .. autoapifunction:: pathml.utils.RGB_to_HSV | |
| .. autoapifunction:: pathml.utils.RGB_to_LAB | |
| .. autoapifunction:: pathml.utils.RGB_to_GREY | |
| .. autoapifunction:: pathml.utils.normalize_matrix_rows | |
| .. autoapifunction:: pathml.utils.normalize_matrix_cols | |
| .. autoapifunction:: pathml.utils.plot_segmentation | |