Add TMA FOV validation functions for user sanity checking

.travis.yml

@@ -23,7 +23,7 @@ cache: pip
 
 script:
   - python -m pip install --editable .
-  - python -m pytest --cov=toffy --pycodestyle toffy
+  - python -m pytest --randomly-seed=42 --randomly-dont-reorganize --cov=toffy --pycodestyle toffy
 
 after_success:
   - coveralls

requirements-test.txt

@@ -1,6 +1,7 @@
 coveralls>=1.8.2,<2.0.0
 pytest<6.0.0
+pytest-cases>=3.6.0,<4
 pytest-cov<3.0.0
 pytest-mock<4.0.0
 pytest-pycodestyle<3.0.0
-pytest-cases>=3.6.0,<4
+pytest-randomly>=3.11.0,<4

templates/autolabel_tma_cores.ipynb

@@ -54,7 +54,7 @@
     "\n",
     "The following input files are required for the script to run:\n",
     "\n",
-    "* `tma_corners_path`: the path to the JSON file containing FOVs defining the upper-left corner and bottom-right corner. It should be named `example_tma_corners.json`, where `example_tma` is replaced with the tma_prefix. \n",
+    "* `tma_corners_path`: the path to the JSON file containing FOVs defining the four corners (top-left, top-right, bottom-left, and bottom-right, in that order). It should be named `example_tma_corners.json`, where `example_tma` is replaced with the `tma_prefix`. \n",
     "* `manual_run_path`: the path to your run file with the manually selected FOVs. It should be named `example_tma_manual_run.json`.\n",
     "* `slide_path`: the path to the slide image of the TMA"
    ]
@@ -157,69 +157,65 @@
   },
   {
    "cell_type": "markdown",
-   "id": "18895a56",
+   "id": "7e0b2449",
    "metadata": {},
    "source": [
-    "### Map proposed tiles to their closest automatically-generated tile (Euclidean)"
+    "### Visualize and remap tiles"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "931a51af",
+   "cell_type": "markdown",
+   "id": "63643da2",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "manual_to_auto_map, manual_fovs_info, auto_fovs_info = tiling_utils.assign_closest_fovs(\n",
-    "    manual_fov_regions,\n",
-    "    auto_fov_regions\n",
-    ")"
+    "Set these parameters to view validation warnings while remapping (mappings are between FOVs in `manual_fov_regions` to FOVs in `auto_fov_regions`):\n",
+    "\n",
+    "* `check_dist`: set to a positive value to notify of FOV mappings at a distance greater than this value (measured in microns), sorted by decreasing distance. Set to `None` to bypass.\n",
+    "* `check_duplicates`: set to `True` to notify of FOVs in `auto_fov_regions` with multiple FOVs mapping to it. Set to `False` to bypass.\n",
+    "* `check_mismatches`: set to `True` to notify of FOV mappings with mismatched names. Set to `False` to bypass."
    ]
   },
   {
-   "cell_type": "markdown",
-   "id": "7e0b2449",
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1fcb1768-7cf9-4aea-90d8-7b6e63d79694",
    "metadata": {},
+   "outputs": [],
    "source": [
-    "### Visualize and remap tiles"
+    "# define which validation checks to display in the FOV pair validation checks box\n",
+    "check_dist = 2000\n",
+    "check_duplicates = True\n",
+    "check_mismatches = True"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "63643da2",
+   "id": "30ee9a89-ed9c-4e45-bcab-83383da8a35d",
    "metadata": {},
    "source": [
-    "Usage notes:\n",
-    "\n",
-    "* Proposed FOVs are drawn in red. Automatically-generated FOVs are drawn in blue.\n",
-    "* The selected proposed FOV and its mapped automatically-generated FOV are colored a darker shade.\n",
-    "* The `Manually-defined FOV` menu can be used to visualize current mappings to automatically-generated FOVs.\n",
-    "* The `Automatically-generated FOV` menu is used for re-mapping a FOV created by this script to one of yours.\n",
-    "* When you're done generating your desired mapping, click the `Save mapping`. This will save your mapping to `mapping_path` specified earlier.\n",
+    "Each FOV in `manual_fov_regions` are mapped to their closest corresponding FOV in `auto_fov_regions` by default. To see the current mappings, select FOVs in the `Manually-defined FOV` menu. To remap a manual FOV to a different auto FOV, use the `Automatically-generated FOV` menu.\n",
     "\n",
-    "Note:\n",
-    "\n",
-    "* The cells after this interactive widget (in the section `Use mapping to rename FOVs in manual_fov_regions`) are only to be run after you're satisfied with the mapping and clicked `Save mapping`.\n",
-    "* Prior to clicking `Save mapping` and re-running the cells in that section, ignore any error messages that may appear in that section.\n",
-    "* If you change your mind after saving the remapped FOVs, you can come back here to redo your mappings, save again, and re-run the code to remap the FOVs."
+    "After you're done finished, click `Save mapping` and run the cells afterward (ignore any error messages that may appear there beforehand). You can always come back here and redo your mappings if you change your mind."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "id": "60fa546d",
    "metadata": {},
    "outputs": [],
    "source": [
     "%matplotlib widget\n",
-    "tiling_utils.interactive_remap(\n",
-    "    manual_to_auto_map,\n",
-    "    manual_fovs_info,\n",
-    "    auto_fovs_info,\n",
+    "tiling_utils.tma_interactive_remap(\n",
+    "    manual_fov_regions,\n",
+    "    auto_fov_regions,\n",
     "    slide_data,\n",
     "    mapping_path,\n",
     "    draw_radius=7,\n",
-    "    figsize=(7, 7)\n",
+    "    figsize=(7, 7),\n",
+    "    check_dist=check_dist,\n",
+    "    check_duplicates=check_duplicates,\n",
+    "    check_mismatches=check_mismatches\n",
     ")"
    ]
   },
@@ -243,17 +239,24 @@
     "    mapping = json.load(mp)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "958dd308-5cdf-4d6f-913f-b40705eb4757",
+   "metadata": {},
+   "source": [
+    "* `randomize`: shuffle the order of the FOVs in `remapped_fov_regions`\n",
+    "* `moly_insert`: insert a Moly point (specified by `moly_path`) between a specified interval of FOVs\n",
+    "* `moly_interval`: if `moly_insert` is set, insert Moly points at this interval"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "840c7372",
    "metadata": {},
    "outputs": [],
    "source": [
-    "# whether to randomize the FOVs in remapped_fov_regions\n",
     "randomize = True\n",
-    "\n",
-    "# whether to insert Moly points between a specified interval of FOVs in remapped_fov_regions\n",
     "moly_insert = True\n",
     "moly_interval = 5"
    ]