robustness against empty data files, new version

Author: vreuter

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).
 
+## [v0.5.6] - 2025-07-17
+
+### Fixed
+* Now empty data files should cause no problem.
+
 ## [v0.5.5] - 2025-05-23
 
 ### Fixed

looptrace_regionals_vis/__init__.py

@@ -10,7 +10,7 @@
 
 from numpydoc_decorator import doc  # type: ignore[import-untyped]
 
-__version__ = "0.5.5"
+__version__ = "0.5.6"
 
 _PACKAGE_NAME = package = Path(__file__).parent.name
 

looptrace_regionals_vis/reader.py

@@ -10,6 +10,7 @@
 import pandas as pd
 from gertils.types import NucleusNumber, TraceIdFrom0
 from numpydoc_decorator import doc  # type: ignore[import-untyped]
+from pandas.errors import EmptyDataError
 
 from .bounding_box import BoundingBox3D
 from .point import FloatLike, Point3D
@@ -119,12 +120,17 @@ def build_layers(folder) -> list[FullDataLayer]:  # type: ignore[no-untyped-def]
         for file_type, file_path in file_by_kind.items():
             logging.debug("Processing data for file type %s: %s", file_type.name, file_path)
             if file_type == InputFileContentType.MergeContributors:
-                rois_by_type = {
-                    MergeContributorRoi: [
-                        _parse_merge_contributor_record(row)
-                        for _, row in pd.read_csv(file_path).iterrows()
+                parse_result: list[MergeContributorRoi]
+                try:
+                    data = pd.read_csv(file_path)
+                except EmptyDataError:
+                    logging.warning("Empty data file: %s", file_path)
+                    parse_result = []
+                else:
+                    parse_result = [
+                        _parse_merge_contributor_record(row) for _, row in data.iterrows()
                     ]
-                }
+                rois_by_type = {MergeContributorRoi: parse_result}
             elif file_type == InputFileContentType.NucleiLabeled:
                 rois_by_type = {}
                 for r in _parse_non_contributor_non_proximal_rois(file_path):
@@ -300,7 +306,12 @@ def _parse_non_contributor_non_proximal_rois(
     path: Path,
 ) -> list[NonNuclearRoi | SingletonRoi | MergedRoi]:
     rois: list[NonNuclearRoi | SingletonRoi | MergedRoi] = []
-    for _, row in pd.read_csv(path).iterrows():
+    try:
+        data = pd.read_csv(path)
+    except EmptyDataError:
+        logging.warning("Empty data file: %s", path)
+        return []
+    for _, row in data.iterrows():
         roiId, time, channel, box, traceId, trace_partners, maybe_nuc_num, maybe_id_and_contribs = (
             _parse_nucleus_labeled_record(row)
         )
@@ -345,7 +356,11 @@ def _parse_non_contributor_non_proximal_rois(
 def _parse_proximity_rejects(
     path: Path,
 ) -> list[tuple[RoiId, set[RoiId], Timepoint, Channel, BoundingBox3D]]:
-    spot_data = pd.read_csv(path, index_col=None)
+    try:
+        spot_data = pd.read_csv(path, index_col=None)
+    except EmptyDataError:
+        logging.warning("Empty data file: %s", path)
+        return []
     return _parse_proximity_rejects_table(spot_data)
 
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "looptrace-regionals-vis"
-version = "0.5.5"
+version = "0.5.6"
 description = "This project facilitates viewing, in `napari`, regional spots from `looptrace`."
 authors = ["Vince Reuter"]
 license = "MIT"