Merge b2581a4 into cd56fac

vanvalenlab · Jul 24, 2020 · 0f40a4a · 0f40a4a
2 parents cd56fac + b2581a4
commit 0f40a4a
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Showing 3 changed files with 20 additions and 2 deletions.
diff --git a/caliban_toolbox/utils/crop_utils.py b/caliban_toolbox/utils/crop_utils.py
@@ -61,7 +61,7 @@ def compute_crop_indices(img_len, crop_size=None, crop_num=None, overlap_frac=0)
     # compute indices based on fixed number of crops
     elif crop_num is not None:
         # number of pixels in non-overlapping portion of crop
-        non_overlap_crop_size = np.ceil(img_len / crop_num)
+        non_overlap_crop_size = np.ceil(img_len / crop_num).astype('int')
 
         # Technically this is the fraction the non-overlap, rather than fraction of the whole,
         # but we're going to visually crop overlays anyway to make sure value is appropriate

diff --git a/caliban_toolbox/utils/crop_utils_test.py b/caliban_toolbox/utils/crop_utils_test.py
@@ -148,6 +148,24 @@ def test_crop_helper():
 
     assert (cropped.shape == (fov_len, stack_len, 30, slice_num, row_crop, col_crop, chan_len))
 
+    # test crops with number specified rather than size
+    row_crop_num, col_crop_num = 5, 6
+    row_starts, row_ends, row_padding = \
+        crop_utils.compute_crop_indices(img_len=row_len, crop_num=row_crop_num,
+                                        overlap_frac=overlap_frac)
+
+    col_starts, col_ends, col_padding = \
+        crop_utils.compute_crop_indices(img_len=col_len, crop_num=col_crop_num,
+                                        overlap_frac=overlap_frac)
+
+    cropped, padded = crop_utils.crop_helper(input_data=test_xr, row_starts=row_starts,
+                                             row_ends=row_ends, col_starts=col_starts,
+                                             col_ends=col_ends,
+                                             padding=(row_padding, col_padding))
+
+    # Because overlap is calculated differently, final size is not exactly equal
+    assert (cropped.shape == (fov_len, stack_len, 30, slice_num, 48, 40, chan_len))
+
     # test that correct region of image is being cropped
     row_crop, col_crop = 40, 40
 

diff --git a/notebooks/Caliban_Figure8_Upload_Combined.ipynb b/notebooks/Caliban_Figure8_Upload_Combined.ipynb
@@ -974,7 +974,7 @@
    "outputs": [],
    "source": [
     "# save cropped data into npz files for upload to Figure8\n",
-    "io_utils.save_npzs_for_caliban(X_data=X_cropped, y_data=y_data, original_data=channel_data, save_dir=save_dir,\n",
+    "io_utils.save_npzs_for_caliban(X_data=X_cropped, y_data=y_cropped, original_data=channel_data, save_dir=save_dir,\n",
     "                                   log_data=log_data)"
    ]
   },