nanoobjectdetection 2.0.0__tar.gz → 2.1.1__tar.gz

{nanoobjectdetection-2.0.0 → nanoobjectdetection-2.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nanoobjectdetection
-Version: 2.0.0
+Version: 2.1.1
 Summary: Particle localization and diffusion analysis for TIFF image stacks
 Author: Tim Stechel, Ronny Förster
 License: MIT

{nanoobjectdetection-2.0.0 → nanoobjectdetection-2.1.1}/nanoobjectdetection/localization.py

@@ -6,21 +6,41 @@ import pandas as pd
 import numpy as np
 import os
 import sys
+import warnings
 from concurrent.futures import ProcessPoolExecutor
 
-def _locate_frame(args):
+
+def _locate_frame(args) -> tuple[pd.DataFrame, bool]:
     import trackpy as tp
 
     frame, diameter, minmass, separation, percentile, preprocess = args
-    return tp.locate(
-        frame,
-        diameter,
-        minmass=minmass,
-        separation=separation,
-        percentile=percentile,
-        preprocess=preprocess,
-        engine="python",
-    )
+    with warnings.catch_warnings(record=True) as caught:
+        warnings.simplefilter("always")
+        found = tp.locate(
+            frame,
+            diameter,
+            minmass=minmass,
+            separation=separation,
+            percentile=percentile,
+            preprocess=preprocess,
+            engine="python",
+        )
+
+    black_image_warning = False
+    for warning in caught:
+        if (
+            warning.category is UserWarning
+            and str(warning.message) == "Image is completely black."
+        ):
+            black_image_warning = True
+        else:
+            warnings.warn_explicit(
+                warning.message,
+                warning.category,
+                warning.filename,
+                warning.lineno,
+            )
+    return found, black_image_warning
 
 
 def locate(
@@ -62,8 +82,17 @@ def locate(
                 results = list(pool.map(_locate_frame, jobs, chunksize=batch))
     else:
         results = [_locate_frame(job) for job in jobs]
+    black_frames = sum(is_black for _, is_black in results)
+    if black_frames:
+        warnings.warn(
+            f"Trackpy found {black_frames} completely black image frame(s). "
+            "If using 8-bit processing, try switching to 16-bit processing. "
+            "The exposure may also have been too low.",
+            UserWarning,
+            stacklevel=2,
+        )
     detections = []
-    for frame_number, found in enumerate(results):
+    for frame_number, (found, _) in enumerate(results):
         if not found.empty:
             found = found.copy()
             found["frame"] = frame_number

{nanoobjectdetection-2.0.0 → nanoobjectdetection-2.1.1}/nanoobjectdetection/pipeline.py

@@ -546,7 +546,11 @@ class AnalysisPipeline:
             )
             maximum = max(maximum, float(np.max(np.maximum(processed, 0.0))))
         if maximum <= 0:
-            raise RuntimeError("Processed image stack contains no positive intensity")
+            raise RuntimeError(
+                "Processed image stack contains no positive intensity; the images "
+                "appear completely black. If using 8-bit processing, try switching "
+                "to 16-bit processing. The exposure may also have been too low."
+            )
         return maximum
 
     @property

{nanoobjectdetection-2.0.0 → nanoobjectdetection-2.1.1}/nanoobjectdetection.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nanoobjectdetection
-Version: 2.0.0
+Version: 2.1.1
 Summary: Particle localization and diffusion analysis for TIFF image stacks
 Author: Tim Stechel, Ronny Förster
 License: MIT

{nanoobjectdetection-2.0.0 → nanoobjectdetection-2.1.1}/nanoobjectdetection.egg-info/SOURCES.txt

@@ -31,5 +31,4 @@ nanoobjectdetection.egg-info/SOURCES.txt
 nanoobjectdetection.egg-info/dependency_links.txt
 nanoobjectdetection.egg-info/entry_points.txt
 nanoobjectdetection.egg-info/requires.txt
-nanoobjectdetection.egg-info/top_level.txt
-nanoobjectdetection_2_0/__init__.py
+nanoobjectdetection.egg-info/top_level.txt

nanoobjectdetection-2.1.1/nanoobjectdetection.egg-info/top_level.txt

@@ -0,0 +1 @@
+nanoobjectdetection

{nanoobjectdetection-2.0.0 → nanoobjectdetection-2.1.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nanoobjectdetection"
-version = "2.0.0"
+version = "2.1.1"
 description = "Particle localization and diffusion analysis for TIFF image stacks"
 readme = "README.md"
 requires-python = ">=3.10"

nanoobjectdetection-2.0.0/nanoobjectdetection.egg-info/top_level.txt

@@ -1,2 +0,0 @@
-nanoobjectdetection
-nanoobjectdetection_2_0

nanoobjectdetection-2.0.0/nanoobjectdetection_2_0/__init__.py

@@ -1,30 +0,0 @@
-"""Backward-compatibility module forwarding to nanoobjectdetection."""
-
-import sys
-import nanoobjectdetection
-
-# Forward package attributes
-__all__ = nanoobjectdetection.__all__
-__version__ = nanoobjectdetection.__version__
-
-for name in __all__:
-    globals()[name] = getattr(nanoobjectdetection, name)
-
-# Ensure submodules imported via `from nanoobjectdetection_2_0.submodule import ...` work
-import importlib
-
-class _CompatibilityFinder:
-    """Redirects imports from nanoobjectdetection_2_0 to nanoobjectdetection."""
-    @classmethod
-    def find_spec(cls, fullname, path=None, target=None):
-        if fullname.startswith("nanoobjectdetection_2_0."):
-            submodule = fullname[len("nanoobjectdetection_2_0."):]
-            try:
-                real_module = importlib.import_module(f"nanoobjectdetection.{submodule}")
-                sys.modules[fullname] = real_module
-                return real_module.__spec__
-            except ImportError:
-                return None
-        return None
-
-sys.meta_path.insert(0, _CompatibilityFinder)