Fix issue in data loading

scale information was not handled properly.
elephant-track · Mar 27, 2024 · aea2f16 · aea2f16
1 parent 9df6134
commit aea2f16
Showing 1 changed file with 30 additions and 35 deletions.
diff --git a/elephant-core/elephant/datasets.py b/elephant-core/elephant/datasets.py
@@ -57,8 +57,7 @@ def profile(func):
         return func
 
 
-def _load_image(za_input, timepoint, use_median=False, img_size=None):
-    img = za_input[timepoint].astype('float32')
+def _load_image(img, use_median=False, img_size=None):
     if use_median and img.ndim == 3:
         global_median = np.median(img)
         for z in range(img.shape[0]):
@@ -86,38 +85,37 @@ def _get_memmap_or_load(za, timepoint, memmap_dir=None, use_median=False,
         fpath = Path(memmap_dir) / f'{key}.dat'
         lock = FileLock(str(fpath) + '.lock')
         with lock:
-            if not fpath.exists():
-                logger().info(f'creating {fpath}')
-                fpath.parent.mkdir(parents=True, exist_ok=True)
+            if not fpath_org.exists():
+                logger().info(f'creating {fpath_org}')
+                fpath_org.parent.mkdir(parents=True, exist_ok=True)
                 img_org = np.memmap(
                     fpath_org,
                     dtype='float32',
                     mode='w+',
                     shape=za.shape[1:]
                 )
                 img_org[:] = za[timepoint].astype('float32')
-                if img_size is None:
-                    img = img_org
-                else:
-                    img = np.memmap(
-                        fpath,
-                        dtype='float32',
-                        mode='w+',
-                        shape=img_size
-                    )
-                    img[:] = F.interpolate(
-                        torch.from_numpy(img_org)[None, None],
-                        size=img_size,
-                        mode='trilinear' if img.ndim == 3 else 'bilinear',
-                        align_corners=True,
-                    )[0, 0].numpy()
-                if use_median and img.ndim == 3:
-                    global_median = np.median(img)
-                    for z in range(img.shape[0]):
-                        slice_median = np.median(img[z])
-                        if 0 < slice_median:
-                            img[z] -= slice_median - global_median
-                img = normalize_zero_one(img)
+            else:
+                img_org = np.memmap(
+                    fpath_org,
+                    dtype='float32',
+                    mode='c',
+                    shape=za.shape[1:]
+                )
+            if not fpath.exists():
+                logger().info(f'creating {fpath}')
+                fpath.parent.mkdir(parents=True, exist_ok=True)
+                img = np.memmap(
+                    fpath,
+                    dtype='float32',
+                    mode='w+',
+                    shape=img_size
+                )
+                img[:] = _load_image(
+                    img_org,
+                    use_median=use_median,
+                    img_size=img_size,
+                )
             logger().info(f'loading from {fpath}')
             return np.memmap(
                 fpath,
@@ -126,14 +124,11 @@ def _get_memmap_or_load(za, timepoint, memmap_dir=None, use_median=False,
                 shape=za.shape[1:] if img_size is None else img_size
             )
     else:
-        img = za[timepoint].astype('float32')
-        if use_median and img.ndim == 3:
-            global_median = np.median(img)
-            for z in range(img.shape[0]):
-                slice_median = np.median(img[z])
-                if 0 < slice_median:
-                    img[z] -= slice_median - global_median
-        img = normalize_zero_one(img)
+        img = _load_image(
+            za[timepoint].astype('float32'),
+            use_median=use_median,
+            img_size=img_size,
+        )
     return img