refactor: move file saving utils to FileHandler

Author: okunator

cellseg_models_pytorch/datasets/dataset_writers/_base_writer.py

@@ -86,7 +86,7 @@ def _get_tiles(
         """Read one image and corresponding masks and do tiling on them."""
         # im, masks = self._get_arrays()
         im = FileHandler.read_img(img_path)
-        masks = FileHandler.read_mask(mask_path, return_all=True)
+        masks = FileHandler.read_mat(mask_path, return_all=True)
 
         if pre_proc is not None:
             masks = pre_proc(masks)

cellseg_models_pytorch/datasets/folder_dataset_train.py

@@ -136,7 +136,7 @@ def read_img_mask(
         """
         out = OrderedDict()
         out["image"] = FileHandler.read_img(self.fnames_imgs[ix])
-        masks = FileHandler.read_mask(self.fnames_masks[ix], return_all=True)
+        masks = FileHandler.read_mat(self.fnames_masks[ix], return_all=True)
 
         try:
             out["inst"] = masks["inst_map"]

cellseg_models_pytorch/postproc/tests/test_postproc.py

@@ -115,7 +115,7 @@ def test_postproc_dran(inst_map):
 
 def test_postproc_stardist(mask_patch_dir):
     mask_path = sorted(mask_patch_dir.glob("*"))[0]
-    inst_map = FileHandler.read_mask(mask_path)
+    inst_map = FileHandler.read_mat(mask_path)
     stardist = gen_stardist_maps(inst_map, 32)
     dist = gen_dist_maps(inst_map)
     rebuild = post_proc_stardist(dist, stardist)