fix #424

gerlichlab · Feb 19, 2025 · 0ed4d08 · 0ed4d08
1 parent 9f0d470
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diff --git a/CHANGELOG.md b/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 will adhere to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.12.1] - 2025-02-19
+
+### Fixed
+* Field of view name matching for cross-channel signal analysis. See [Issue 424](https://github.com/gerlichlab/looptrace/issues/424).
+
 ## [v0.12.0] - 2025-02-18
 
 ### Added
@@ -30,6 +35,9 @@ __Dependency changes (non-exhaustive)__:
 * Bumped the lower bound on the `nd2` dependency up from 0.5.3 to 0.10.1. See [Issue 423](https://github.com/gerlichlab/looptrace/issues/423).
 * `os-lib` is now at version 0.11.3.
 
+### Known Issues
+* Cross-channel signal analysis won't work. See [Issue 424](https://github.com/gerlichlab/looptrace/issues/424).
+
 ## [v0.11.3] - 2024-12-03
 
 ### Fixed

diff --git a/Dockerfile b/Dockerfile
@@ -15,7 +15,7 @@ RUN apt-get update -y && \
 RUN mkdir /looptrace
 WORKDIR /looptrace
 COPY . /looptrace
-RUN mv /looptrace/target/scala-3.5.2/looptrace-assembly-0.12.0.jar /looptrace/looptrace
+RUN mv /looptrace/target/scala-3.5.2/looptrace-assembly-0.12.1.jar /looptrace/looptrace
 
 # Install new-ish R and necessary packages.
 RUN echo "Installing R..." && \

diff --git a/bin/cli/run_signal_analysis.py b/bin/cli/run_signal_analysis.py
@@ -181,6 +181,7 @@ def workflow(
                         by_raw_channel: Mapping[int, list[dict]] = defaultdict(list)
                         # TODO: refactor with https://github.com/gerlichlab/gertils/issues/32
                         for fov, raw_img in N.iterate_over_pairs_of_fov_name_and_original_image():
+                            fov: str = fov.removesuffix(".zarr")
                             img = raw_img.compute()
                             logging.info(f"Analysing signal for FOV: {fov}")
                             nuc_drift: DriftRecord = all_nuclei_drifts[fov]
@@ -244,10 +245,10 @@ def read_drift_file(drift_file: Path, get_key: Callable[[pd.Series], _K]) -> Map
 
 
 read_signal_drifts_file: Callable[[Path], Mapping[FieldOfViewName, "DriftRecord"]] = \
-    read_drift_file(lambda row: row[FIELD_OF_VIEW_COLUMN])
+    read_drift_file(lambda row: row[FIELD_OF_VIEW_COLUMN].removesuffix(".zarr"))
 
 read_spot_drifts_file: Callable[[Path], Mapping[tuple[FieldOfViewName, RawTimepoint], "DriftRecord"]] = \
-    read_drift_file(lambda row: (row[FIELD_OF_VIEW_COLUMN], row[TIMEPOINT_COLUMN]))
+    read_drift_file(lambda row: (row[FIELD_OF_VIEW_COLUMN].removesuffix(".zarr"), row[TIMEPOINT_COLUMN]))
 
 
 

diff --git a/build.sbt b/build.sbt
@@ -8,7 +8,7 @@ val primaryJavaVersion = "11"
 val primaryOs = "ubuntu-latest"
 val isPrimaryOsAndPrimaryJavaTest = s"runner.os == '$primaryOs' && runner.java-version == '$primaryJavaVersion'"
 ThisBuild / scalaVersion     := "3.5.2"
-ThisBuild / version          := "0.12.0"
+ThisBuild / version          := "0.12.1"
 ThisBuild / organization     := orgName
 ThisBuild / organizationName := "Gerlich Group, IMBA, OEAW"
 

diff --git a/looptrace/__init__.py b/looptrace/__init__.py
@@ -22,7 +22,7 @@
 
 
 # This is put into place by the docker build, as declared in the Dockerfile.
-LOOPTRACE_JAR_PATH = importlib.resources.files(__name__).joinpath("looptrace-assembly-0.12.0.jar")
+LOOPTRACE_JAR_PATH = importlib.resources.files(__name__).joinpath("looptrace-assembly-0.12.1.jar")
 LOOPTRACE_JAVA_PACKAGE = "at.ac.oeaw.imba.gerlich.looptrace"
 
 FIELD_OF_VIEW_COLUMN = "fieldOfView"

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "looptrace"
-version = "0.12.0"
+version = "0.12.1"
 description = "Library and programs for tracing chromatin loops from microscopy images"
 authors = [
     "Kai Sandvold Beckwith",