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angelolab · Aug 15, 2023 · 8c34b21 · 8c34b21
1 parent bbbd026
commit 8c34b21
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Showing 3 changed files with 19 additions and 8 deletions.
diff --git a/src/toffy/image_stitching.py b/src/toffy/image_stitching.py
@@ -283,6 +283,7 @@ def fix_image_resolutions(resolution_data, extraction_dir):
  tiff_data = load_utils.load_imgs_from_tree(extraction_dir, fovs=[fov])
 
  # scale and save every channel image
+ print(f"Changing {fov} from {tiff_data.shape[1]} to {tiff_data.shape[1]*scale}.")
  for channel in tiff_data.channels.values:
  channel_data = tiff_data.loc[fov, :, :, channel]
  rescale = rescale_image(

diff --git a/templates/3f_check_resolutions.ipynb b/templates/3f_check_resolutions.ipynb
@@ -50,7 +50,7 @@
  "id": "b4edefe7-7f3a-4883-bcb3-47158753c837",
  "metadata": {},
  "source": [
- "### Step 1: Check resolutions"
+ "**Step 1: Check resolutions**"
  ]
  },
  {
@@ -65,13 +65,20 @@
  ]
  },
  {
- "cell_type": "code",
- "execution_count": null,
- "id": "cc4eade1-9fad-458f-92cf-8beebed0209f",
- "metadata": {},
- "outputs": [],
+ "cell_type": "markdown",
+ "id": "4dd4ce41-a637-4358-abdd-2d333a64e4d8",
+ "metadata": {
+ "execution": {
+ "iopub.execute_input": "2023-08-15T18:57:42.867715Z",
+ "iopub.status.busy": "2023-08-15T18:57:42.866942Z",
+ "iopub.status.idle": "2023-08-15T18:57:42.879774Z",
+ "shell.execute_reply": "2023-08-15T18:57:42.878978Z",
+ "shell.execute_reply.started": "2023-08-15T18:57:42.867666Z"
+ },
+ "tags": []
+ },
  "source": [
- "### Step 2: Chane resolutions"
+ "**Step 2: Change image sizes**"
  ]
  },
  {

diff --git a/tests/image_stitching_test.py b/tests/image_stitching_test.py
@@ -322,12 +322,15 @@ def test_fix_image_resolutions(mocked_print):
  )
  image_stitching.fix_image_resolutions(extra_data, tmpdir)
  mocked_print.mock_calls == [call("No resolution scaling needed for any FOVs in this run.")]
+ mocked_print.reset_mock()
 
  # test image resolution change
  resolution_data = pd.DataFrame(
- {"fov": fov_list, "pixels / 400 microns": [512, 1024, 512, 256]}
+ {"fov": fov_list, "pixels / 400 microns": [1024, 2048, 1024, 512]}
  )
  image_stitching.fix_image_resolutions(resolution_data, tmpdir)
+ mocked_print.mock_calls[0] == call("Changing fov-2-scan-1 from 10 to 5.")
+ mocked_print.mock_calls[1] == call("Changing fov-4-scan-1 from 10 to 20.")
 
  # check downscale for fov 2
  tiff_data = load_utils.load_imgs_from_tree(tmpdir, fovs=["fov-2-scan-1"])