FOV resolution check

src/toffy/json_utils.py

@@ -3,6 +3,7 @@
 import os
 import warnings
 
+import pandas as pd
 from alpineer import io_utils
 
 
@@ -194,3 +195,48 @@ def check_for_empty_files(bin_file_dir):
 
     # return the list of fov names
     return empty_json_files
+
+
+def check_fov_resolutions(bin_file_dir, run_name, save_path=None):
+    """Use the run metadata to calculate the resolution of each fov
+    Args:
+        bin_file_dir (str): directory containing the run json file
+        run_name (str): name of the run and corresponding run file
+        save_path (str): path to save data to, default None doesn't write data out
+
+    Returns:
+        pd.DataFrame: details fov names and corresponding resolution value
+    """
+    # read in run metadata
+    run_file_path = os.path.join(bin_file_dir, run_name + ".json")
+    io_utils.validate_paths([run_file_path])
+    run_metadata = read_json_file(run_file_path, encoding="utf-8")
+
+    fov_names, custom_names, resolutions = [], [], []
+    for fov in run_metadata.get("fovs", ()):
+        # get fov names
+        fov_number = fov.get("runOrder")
+        default_name = f"fov-{fov_number}-scan-1"
+        custom_name = fov.get("name")
+        fov_names.append(default_name)
+        custom_names.append(custom_name)
+
+        # retrieve pixel and micron specs
+        fov_pixel_length = fov.get("frameSizePixels")["width"]
+        fov_micron_length = fov.get("fovSizeMicrons")
+
+        # calculate and save fov resolution per 400 microns
+        mult = 400 / fov_micron_length
+        pixels_adj = int(mult * fov_pixel_length)
+
+        # output values
+        print(f"{default_name} ({custom_name}): {pixels_adj} pixels x {400} microns")
+        resolutions.append(pixels_adj)
+
+    resolution_data = pd.DataFrame(
+        {"fov": fov_names, "name": custom_names, "pixels / 400 microns": resolutions}
+    )
+    if save_path:
+        resolution_data.to_csv(save_path, index=False)
+
+    return resolution_data

templates/3f_check_resolutions.ipynb

@@ -0,0 +1,79 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "4857c47b-f476-4494-9a0d-742ef35c0a85",
+   "metadata": {},
+   "source": [
+    "# Check FOV Resolutions\n",
+    "This notebook will use the run file to check the image resolution for each FOV in the run. Consistent resolution level is important for downstream processing."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "353ffbc5-4784-49e1-9fd5-f1344d7892da",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "from toffy.json_utils import check_fov_resolutions"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "cd7ff391-2d75-4098-bd9d-4d98e07d45ba",
+   "metadata": {},
+   "source": [
+    "## Required variables\n",
+    "You will need to define the following argument for this notebook.\n",
+    " - `run_name` should contain the exact name of the MIBI run to extract from"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4b81ca96-e7dc-4603-87ce-284edeb2d423",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# set up args for current run\n",
+    "run_name = 'YYYY-MM-DD_run_name'\n",
+    "\n",
+    "bin_file_dir = os.path.join('D:\\\\Data', run_name)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b30a4058-4976-4bdc-9714-f9babe056d85",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# check resolutions \n",
+    "resolution_data = check_fov_resolutions(bin_file_dir, run_name, save_path=None)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "toffy_env",
+   "language": "python",
+   "name": "toffy_env"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

tests/json_utils_test.py

@@ -184,3 +184,51 @@ def test_check_for_empty_files():
             empty_files = json_utils.check_for_empty_files(temp_dir)
 
         assert empty_files == ["empty_file"]
+
+
+def test_check_fov_resolutions():
+    with tempfile.TemporaryDirectory() as temp_dir:
+        run_data = {
+            "fovs": [
+                {
+                    "runOrder": 1,
+                    "scanCount": 1,
+                    "frameSizePixels": {"width": 32, "height": 32},
+                    "fovSizeMicrons": 100,
+                },
+                {
+                    "runOrder": 2,
+                    "scanCount": 1,
+                    "frameSizePixels": {"width": 32, "height": 32},
+                    "fovSizeMicrons": 100,
+                },
+                {
+                    "runOrder": 3,
+                    "scanCount": 1,
+                    "frameSizePixels": {"width": 16, "height": 16},
+                    "fovSizeMicrons": 100,
+                },
+            ],
+        }
+
+        json_utils.write_json_file(os.path.join(temp_dir, "test_run.json"), run_data)
+
+        # test successful resolution check
+        resolution_data = json_utils.check_fov_resolutions(
+            temp_dir, "test_run", save_path=os.path.join(temp_dir, "resolution_data.csv")
+        )
+
+        assert resolution_data.shape == (3, 3)
+        assert (
+            np.array(["fov-1-scan-1", "fov-2-scan-1", "fov-3-scan-1"]) == resolution_data["fov"]
+        ).all()
+        assert (
+            resolution_data["pixels / 400 microns"].iloc[0]
+            == resolution_data["pixels / 400 microns"].iloc[1]
+        )
+        assert (
+            resolution_data["pixels / 400 microns"].iloc[0]
+            != resolution_data["pixels / 400 microns"].iloc[2]
+        )
+
+        assert os.path.exists(os.path.join(temp_dir, "resolution_data.csv"))