Fix for nuclear speckle image display in CytoDataFrame (#64)

* dynamic bounding box and scale image bit depth * add opencv * check images for adjustment; add tests * linting * coverage configuration * add note about configuration * fix coverage badge reference for pypi * move to emoji character instead of code for pypi * more descriptive parameter name Co-Authored-By: Jenna Tomkinson <[email protected]> * fix tests * format before lint --------- Co-authored-by: Jenna Tomkinson <[email protected]>
WayScience · Aug 5, 2024 · af7afdf · af7afdf
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diff --git a/.gitignore b/.gitignore
@@ -142,3 +142,5 @@ cython_debug/
 *.csv
 
 .DS_Store
+
+tests/data/cytotable/Nuclear_speckles
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -51,8 +51,8 @@ repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: "v0.5.5"
     hooks:
-      - id: ruff
       - id: ruff-format
+      - id: ruff
   - repo: local
     hooks:
       - id: code-cov-gen

diff --git a/README.md b/README.md
@@ -4,11 +4,11 @@
 
 ![PyPI - Version](https://img.shields.io/pypi/v/cosmicqc)
 [![Build Status](https://github.com/WayScience/coSMicQC/actions/workflows/run-tests.yml/badge.svg?branch=main)](https://github.com/WayScience/coSMicQC/actions/workflows/run-tests.yml?query=branch%3Amain)
-![Coverage Status](./media/coverage-badge.svg)
+![Coverage Status](https://raw.githubusercontent.com/WayScience/coSMicQC/main/media/coverage-badge.svg)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![Poetry](https://img.shields.io/endpoint?url=https://python-poetry.org/badge/v0.json)](https://python-poetry.org/)
 
-> :stars: Navigate the cosmos of single-cell morphology with confidence — coSMicQC keeps your data on course!
+> 🌠 Navigate the cosmos of single-cell morphology with confidence — coSMicQC keeps your data on course!
 
 coSMicQC is a Python package to evaluate converted single-cell morphology outputs from CytoTable.
 

diff --git a/media/coverage-badge.svg b/media/coverage-badge.svg
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -32,6 +32,7 @@ pywavelets = [
   {version = "^1.4.1", python = "<3.9"},
   {version = ">1.4.1", python = ">=3.9"}
 ] # dependency of scikit-image
+opencv-python = "^4.10.0.84" # used for image modifications in cytodataframe
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.2.0" # provides testing capabilities for project
@@ -96,6 +97,14 @@ markers = [
     "generate_report_image: tests which involve the creation of report images.",
 ]
 
+[tool.coverage.run]
+# settings to avoid errors with cv2 and coverage
+# see here for more: https://github.com/nedbat/coveragepy/issues/1653
+omit = [
+    "config.py",
+    "config-3.py",
+]
+
 # set dynamic versioning capabilities for project
 [tool.poetry-dynamic-versioning]
 enable = true

diff --git a/src/cosmicqc/frame.py b/src/cosmicqc/frame.py
@@ -27,6 +27,8 @@
 import plotly.express as px
 import plotly.graph_objects as go
 import skimage
+import skimage.io
+import skimage.measure
 from IPython import get_ipython
 from jinja2 import Environment, FileSystemLoader
 from pandas._config import (
@@ -37,6 +39,8 @@
 )
 from PIL import Image, ImageDraw
 
+from .image import adjust_image_brightness, is_image_too_dark
+
 # provide backwards compatibility for Self type in earlier Python versions.
 # see: https://peps.python.org/pep-0484/#annotating-instance-and-class-methods
 CytoDataFrame_type = TypeVar("CytoDataFrame_type", bound="CytoDataFrame")
@@ -628,7 +632,17 @@ def draw_outline_on_image(actual_image_path: str, mask_image_path: str) -> Image
         # Load the TIFF image
         tiff_image_array = skimage.io.imread(actual_image_path)
         # Convert to PIL Image and then to 'RGBA'
-        tiff_image = Image.fromarray(np.uint8(tiff_image_array)).convert("RGBA")
+
+        # Check if the image is 16-bit and grayscale
+        if tiff_image_array.dtype == np.uint16:
+            # Normalize the image to 8-bit for display purposes
+            tiff_image_array = (tiff_image_array / 256).astype(np.uint8)
+
+        tiff_image = Image.fromarray(tiff_image_array).convert("RGBA")
+
+        # Check if the image is too dark and adjust brightness if needed
+        if is_image_too_dark(tiff_image):
+            tiff_image = adjust_image_brightness(tiff_image)
 
         # Load the mask image and convert it to grayscale
         mask_image = Image.open(mask_image_path).convert("L")
@@ -659,19 +673,20 @@ def process_image_data_as_html_display(
         bounding_box: Tuple[int, int, int, int],
     ) -> str:
         if not pathlib.Path(data_value).is_file():
-            if not pathlib.Path(
-                candidate_path := (
-                    f"{self._custom_attrs['data_context_dir']}/{data_value}"
-                )
-            ).is_file():
-                return data_value
+            # Use rglob to recursively search for a matching file
+            if candidate_paths := list(
+                pathlib.Path(self._custom_attrs["data_context_dir"]).rglob(data_value)
+            ):
+                # if we find a candidate, return the first one
+                candidate_path = candidate_paths[0]
             else:
-                pass
+                # we don't have any candidate paths so return the unmodified value
+                return data_value
 
         try:
             if self._custom_attrs["data_mask_context_dir"] is not None and (
                 matching_mask_file := list(
-                    pathlib.Path(self._custom_attrs["data_mask_context_dir"]).glob(
+                    pathlib.Path(self._custom_attrs["data_mask_context_dir"]).rglob(
                         f"{pathlib.Path(candidate_path).stem}*"
                     )
                 )
@@ -773,15 +788,46 @@ def _repr_html_(
             # gather indices which will be displayed based on pandas configuration
             display_indices = self.get_displayed_rows()
 
+            # gather bounding box columns for use below
+            bounding_box_cols = self._custom_attrs["data_bounding_box"].columns.tolist()
+
             for image_col in image_cols:
                 data.loc[display_indices, image_col] = data.loc[display_indices].apply(
                     lambda row: self.process_image_data_as_html_display(
                         data_value=row[image_col],
                         bounding_box=(
-                            row["Cytoplasm_AreaShape_BoundingBoxMinimum_X"],
-                            row["Cytoplasm_AreaShape_BoundingBoxMinimum_Y"],
-                            row["Cytoplasm_AreaShape_BoundingBoxMaximum_X"],
-                            row["Cytoplasm_AreaShape_BoundingBoxMaximum_Y"],
+                            # rows below are specified using the column name to
+                            # determine which part of the bounding box the columns
+                            # relate to (the list of column names could be in
+                            # various order).
+                            row[
+                                next(
+                                    col
+                                    for col in bounding_box_cols
+                                    if "Minimum_X" in col
+                                )
+                            ],
+                            row[
+                                next(
+                                    col
+                                    for col in bounding_box_cols
+                                    if "Minimum_Y" in col
+                                )
+                            ],
+                            row[
+                                next(
+                                    col
+                                    for col in bounding_box_cols
+                                    if "Maximum_X" in col
+                                )
+                            ],
+                            row[
+                                next(
+                                    col
+                                    for col in bounding_box_cols
+                                    if "Maximum_Y" in col
+                                )
+                            ],
                         ),
                     ),
                     axis=1,

diff --git a/src/cosmicqc/image.py b/src/cosmicqc/image.py
@@ -0,0 +1,66 @@
+"""
+Helper functions for working with images in the context of coSMicQC.
+"""
+
+import cv2
+import numpy as np
+from PIL import Image, ImageEnhance
+
+
+def is_image_too_dark(image: Image, pixel_brightness_threshold: float = 10.0) -> bool:
+    """
+    Check if the image is too dark based on the mean brightness.
+    By "too dark" we mean not as visible to the human eye.
+
+    Args:
+        image (Image):
+            The input PIL Image.
+        threshold (float):
+            The brightness threshold below which the image is considered too dark.
+
+    Returns:
+        bool:
+            True if the image is too dark, False otherwise.
+    """
+    # Convert the image to a numpy array and then to grayscale
+    img_array = np.array(image)
+    gray_image = cv2.cvtColor(img_array, cv2.COLOR_RGBA2GRAY)
+
+    # Calculate the mean brightness
+    mean_brightness = np.mean(gray_image)
+
+    return mean_brightness < pixel_brightness_threshold
+
+
+def adjust_image_brightness(image: Image) -> Image:
+    """
+    Adjust the brightness of an image using histogram equalization.
+
+    Args:
+        image (Image):
+            The input PIL Image.
+
+    Returns:
+        Image:
+            The brightness-adjusted PIL Image.
+    """
+    # Convert the image to numpy array and then to grayscale
+    img_array = np.array(image)
+    gray_image = cv2.cvtColor(img_array, cv2.COLOR_RGBA2GRAY)
+
+    # Apply histogram equalization to improve the contrast
+    equalized_image = cv2.equalizeHist(gray_image)
+
+    # Convert back to RGBA
+    img_array[:, :, 0] = equalized_image  # Update only the R channel
+    img_array[:, :, 1] = equalized_image  # Update only the G channel
+    img_array[:, :, 2] = equalized_image  # Update only the B channel
+
+    # Convert back to PIL Image
+    enhanced_image = Image.fromarray(img_array)
+
+    # Slightly reduce the brightness
+    enhancer = ImageEnhance.Brightness(enhanced_image)
+    reduced_brightness_image = enhancer.enhance(0.7)
+
+    return reduced_brightness_image
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -7,9 +7,11 @@
 import pathlib
 
 import cosmicqc
+import numpy as np
 import pandas as pd
 import plotly.colors as pc
 import pytest
+from PIL import Image
 
 
 @pytest.fixture(name="cytotable_CFReT_data_df")
@@ -127,3 +129,24 @@ def fixture_generate_show_report_html_output(cytotable_CFReT_data_df: pd.DataFra
     )
 
     return report_path
+
+
+@pytest.fixture
+def fixture_dark_image():
+    # Create a dark image (50x50 pixels, almost black)
+    dark_img_array = np.zeros((50, 50, 3), dtype=np.uint8)
+    return Image.fromarray(dark_img_array)
+
+
+@pytest.fixture
+def fixture_mid_brightness_image():
+    # Create an image with medium brightness (50x50 pixels, mid gray)
+    mid_brightness_img_array = np.full((50, 50, 3), 128, dtype=np.uint8)
+    return Image.fromarray(mid_brightness_img_array)
+
+
+@pytest.fixture
+def fixture_bright_image():
+    # Create a bright image (50x50 pixels, almost white)
+    bright_img_array = np.full((50, 50, 3), 255, dtype=np.uint8)
+    return Image.fromarray(bright_img_array)
diff --git a/tests/test_image.py b/tests/test_image.py
@@ -0,0 +1,42 @@
+"""
+Tests cosmicqc image module
+"""
+
+from cosmicqc.image import adjust_image_brightness, is_image_too_dark
+from PIL import Image
+
+
+def test_is_image_too_dark_with_dark_image(fixture_dark_image: Image):
+    assert is_image_too_dark(fixture_dark_image, pixel_brightness_threshold=10.0)
+
+
+def test_is_image_too_dark_with_bright_image(fixture_bright_image: Image):
+    assert not is_image_too_dark(fixture_bright_image, pixel_brightness_threshold=10.0)
+
+
+def test_is_image_too_dark_with_mid_brightness_image(
+    fixture_mid_brightness_image: Image,
+):
+    assert not is_image_too_dark(
+        fixture_mid_brightness_image, pixel_brightness_threshold=10.0
+    )
+
+
+def test_adjust_image_brightness_with_dark_image(fixture_dark_image: Image):
+    adjusted_image = adjust_image_brightness(fixture_dark_image)
+    # we expect that image to be too dark (it's all dark, so there's no adjustments)
+    assert is_image_too_dark(adjusted_image, pixel_brightness_threshold=10.0)
+
+
+def test_adjust_image_brightness_with_bright_image(fixture_bright_image: Image):
+    adjusted_image = adjust_image_brightness(fixture_bright_image)
+    # Since the image was already bright, it should remain bright
+    assert not is_image_too_dark(adjusted_image, pixel_brightness_threshold=10.0)
+
+
+def test_adjust_image_brightness_with_mid_brightness_image(
+    fixture_mid_brightness_image: Image,
+):
+    adjusted_image = adjust_image_brightness(fixture_mid_brightness_image)
+    # The image should still not be too dark after adjustment
+    assert not is_image_too_dark(adjusted_image, pixel_brightness_threshold=10.0)