Merge pull request #57 from RolnickLab/feat/update-export-collection

Add species labels to exported crops

trapdata/cli/export.py

@@ -24,7 +24,7 @@
  get_monitoring_session_images,
  get_monitoring_sessions_from_db,
 )
-from trapdata.db.models.occurrences import list_occurrences
+from trapdata.db.models.occurrences import Occurrence, list_occurrences
 
 cli = typer.Typer(no_args_is_help=True)
 
@@ -88,7 +88,8 @@ def occurrences(
  events = get_monitoring_sessions_from_db(
  db_path=settings.database_url, base_directory=settings.image_base_path
  )
- occurrences = []
+
+ occurrences: list[Occurrence] = []
 
  tabular_formats = [ExportFormat.csv]
  plain_text_formats = [ExportFormat.csv, ExportFormat.html]
@@ -106,32 +107,36 @@ def occurrences(
  )
  logger.info(f"Preparing to export {len(occurrences)} records as {format}")
 
+ if outfile:
+ destination_dir = outfile.parent
+ else:
+ destination_dir = settings.user_data_path / "exports"
+ destination_dir.mkdir(parents=True, exist_ok=True)
+
  if collect_images:
  # Collect images for exported occurrences into a subdirectory
- subdir = "exports"
  if outfile:
  name = outfile.stem
  else:
  name = f"occurrences_{int(time.time())}"
- destination_dir = settings.user_data_path / subdir / f"{name}_images"
+ destination_dir = destination_dir / f"{name}_images"
  logger.info(f'Collecting images into "{destination_dir}"')
  destination_dir.mkdir(parents=True, exist_ok=True)
- else:
- destination_dir = None
 
- for occurrence in occurrences:
- for example in occurrence.examples:
- path = pathlib.Path(example["cropped_image_path"]).resolve()
- if destination_dir:
- destination = destination_dir / f"{occurrence.id}-{path.name}"
+ for occurrence in occurrences:
+ for example in occurrence.examples:
+ path = pathlib.Path(example["cropped_image_path"]).resolve()
+ destination = (
+ destination_dir / f"{occurrence.label} {occurrence.id} {path.name}"
+ )
  if not destination.exists():
  shutil.copy(path, destination)
  path = destination
- if absolute_paths:
- final_path = path.absolute()
- else:
- final_path = path.relative_to(settings.user_data_path)
- example["cropped_image_path"] = final_path
+  if absolute_paths:
+  final_path = path.absolute()
+  else:
+  final_path = path.relative_to(destination_dir)
+  example["cropped_image_path"] = final_path
 
  if format in tabular_formats:
  for occurrence in occurrences: