initial pass at new version to support camel case naming downstream

CHANGELOG.md

@@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## Unreleased
+
+### Changed
+* Renaming `mean_intensity` to `meanIntensity` right away after detection, before writing to disk.
+
 ## [v0.1.0] - 2024-04-18
 
 ### Added

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "spotfishing"
-version = "0.1.0"
+version = "0.2.0"
 description = "Detecting spots in FISH images"
 authors = [
     "Vince Reuter <[email protected]>",

spotfishing/__init__.py

@@ -1,6 +1,6 @@
 """Package-level members"""
 
-from ._constants import ROI_AREA_KEY, ROI_MEAN_INTENSITY_KEY
+from ._constants import ROI_AREA_KEY, ROI_MEAN_INTENSITY_KEY, ROI_MEAN_INTENSITY_KEY_CAMEL_CASE
 from ._exceptions import *
 from .detection_result import DetectionResult, RoiCenterKeys
 from .detectors import detect_spots_dog, detect_spots_int
@@ -11,7 +11,7 @@
 
 __all__ = [
     "ROI_AREA_KEY",
-    "ROI_MEAN_INTENSITY_KEY",
+    "ROI_MEAN_INTENSITY_KEY_CAMEL_CASE", # Only export this (not the snake case one).
     "DifferenceOfGaussiansTransformation",
     "DimensionalityError",
     "RoiCenterKeys",

spotfishing/_constants.py

@@ -1,13 +1,13 @@
-"""Constant useful package-wide"""
+"""Constants useful package-wide"""
 
 __author__ = "Vince Reuter"
 __credits__ = ["Vince Reuter"]
 
 __all__ = [
     "ROI_AREA_KEY",
     "ROI_CENTROID_KEY",
-    "ROI_LABEL_KEY",
-    "ROI_MEAN_INTENSITY_KEY",
+    "ROI_MEAN_INTENSITY_KEY", # Export this for package-internal use.
+    "ROI_MEAN_INTENSITY_KEY_CAMEL_CASE",
 ]
 
 
@@ -17,8 +17,7 @@
 # the key for an ROI's centroid, coming back from skimage.measure.regionprops_table
 ROI_CENTROID_KEY = "centroid_weighted"
 
-# the key for an ROI's label, coming back from skimage.measure.regionprops_table
-ROI_LABEL_KEY = "label"
-
 # the key for an ROI's average intensity, coming back from skimage.measure.regionprops_table
 ROI_MEAN_INTENSITY_KEY = "intensity_mean"
+
+ROI_MEAN_INTENSITY_KEY_CAMEL_CASE = "intensityMean"

spotfishing/detection_result.py

@@ -30,21 +30,21 @@ def to_list(cls) -> list[str]:
 
 # how to rename columns arising from extraction from skimage.measure.regionprops_table, to better suit downstream analysis
 # TODO: consider making this configurable, see: https://github.com/gerlichlab/spotfishing/issues/1
-ROI_CENTROID_COLUMN_RENAMING = tuple(
+SPOT_DETECTION_COLUMN_RENAMING: tuple[str, str] = tuple(
     (f"{ROI_CENTROID_KEY}-{i}", c) for i, c in enumerate(RoiCenterKeys.to_list())
-)
+) + (ROI_MEAN_INTENSITY_KEY, ROI_MEAN_INTENSITY_KEY_CAMEL_CASE)
 
 # fields to pull from skimage.measure.regionprops_table result, besides centroid coordinates and label
 ROI_MEASUREMENT_KEYS = [ROI_AREA_KEY, ROI_MEAN_INTENSITY_KEY]
 
 # the sequence of columns of fields extracted from skimage.measure.regionprops_table, after accounting for expansion in multiple dimensions (e.g., centroid_weighted)
 SKIMAGE_REGIONPROPS_TABLE_COLUMNS_EXPANDED = [
-    old for old, _ in ROI_CENTROID_COLUMN_RENAMING
+    old for old, _ in SPOT_DETECTION_COLUMN_RENAMING
 ] + ROI_MEASUREMENT_KEYS
 
 # the expected column names in a detection result table, after extraction and renaming
 DETECTION_RESULT_TABLE_COLUMNS = [
-    dict(ROI_CENTROID_COLUMN_RENAMING).get(c, c)
+    dict(SPOT_DETECTION_COLUMN_RENAMING).get(c, c)
     for c in SKIMAGE_REGIONPROPS_TABLE_COLUMNS_EXPANDED
 ]
 

spotfishing/detectors.py

@@ -17,7 +17,7 @@
 from ._exceptions import DimensionalityError
 from ._types import *
 from .detection_result import (
-    ROI_CENTROID_COLUMN_RENAMING,
+    SPOT_DETECTION_COLUMN_RENAMING,
     ROI_MEASUREMENT_KEYS,
     SKIMAGE_REGIONPROPS_TABLE_COLUMNS_EXPANDED,
     DetectionResult,
@@ -125,13 +125,14 @@ def _build_props_table(
             regionprops_table(
                 label_image=labels,
                 intensity_image=input_image,
-                properties=tuple(
-                    [ROI_LABEL_KEY, ROI_CENTROID_KEY] + ROI_MEASUREMENT_KEYS
-                ),
+                properties=(ROI_CENTROID_KEY, *ROI_MEASUREMENT_KEYS),
             )
         )
-    spot_props = spot_props.drop(["label"], axis=1, errors="ignore")
-    spot_props = spot_props.rename(columns=dict(ROI_CENTROID_COLUMN_RENAMING))
+    spot_props = spot_props.rename(
+        columns=dict(SPOT_DETECTION_COLUMN_RENAMING),
+        inplace=False,
+        errors="raise",
+    )
     spot_props = spot_props.reset_index(drop=True)
     return spot_props, labels