dcnum 0.20.0__tar.gz → 0.20.1__tar.gz

{dcnum-0.20.0 → dcnum-0.20.1}/CHANGELOG

@@ -1,3 +1,6 @@
+0.20.1
+ - fix: relative basin locations not written correctly
+ - enh: increase deque size threshold for waiting for writer
 0.20.0
  - feat: support reading mapped basins
  - feat: support writing mapped-basin-based output files

{dcnum-0.20.0/src/dcnum.egg-info → dcnum-0.20.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.20.0
+Version: 0.20.1
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.20.0 → dcnum-0.20.1}/src/dcnum/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.20.0'
-__version_tuple__ = version_tuple = (0, 20, 0)
+__version__ = version = '0.20.1'
+__version_tuple__ = version_tuple = (0, 20, 1)

{dcnum-0.20.0 → dcnum-0.20.1}/src/dcnum/feat/event_extractor_manager_thread.py

@@ -96,8 +96,8 @@ class EventExtractorManagerThread(threading.Thread):
             # If the writer_dq starts filling up, then this could lead to
             # an oom-kill signal. Stall for the writer to prevent this.
             ldq = len(self.writer_dq)
-            if ldq > 100:
-                stallsec = ldq / 100
+            if ldq > 1000:
+                stallsec = ldq / 1000
                 self.logger.warning(
                     f"Stalling {stallsec:.1f}s for slow writer")
                 time.sleep(stallsec)

{dcnum-0.20.0 → dcnum-0.20.1}/src/dcnum/logic/ctrl.py

@@ -613,7 +613,7 @@ class DCNumJobRunner(threading.Thread):
                     self.logger.debug(f"Creating basin for {feats}")
                     # Relative and absolute paths.
                     pin = pathlib.Path(hin.filename).resolve()
-                    pout = pathlib.Path(hout.filename).resolve()
+                    pout = pathlib.Path(hout.filename).resolve().parent
                     paths = [pin, os.path.relpath(pin, pout)]
                     hw.store_basin(name="dcnum basin",
                                    features=feats,

{dcnum-0.20.0 → dcnum-0.20.1}/src/dcnum/read/const.py

@@ -8,7 +8,7 @@ PROTECTED_FEATURES = [
     "pressure",
     "temp",
     "temp_amb",
-    "time"
+    "time",
 ]
 
 # User-defined features may be anything, but if the user needs something

{dcnum-0.20.0 → dcnum-0.20.1/src/dcnum.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.20.0
+Version: 0.20.1
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.20.0 → dcnum-0.20.1}/tests/test_logic_pipeline.py

@@ -88,6 +88,45 @@ def test_basin_strategy_tap():
         assert "image" in hd
 
 
+def test_basin_relative_path():
+    path_orig = retrieve_data("fmt-hdf5_cytoshot_full-features_2023.zip")
+    path = path_orig.with_name("input.rtdc")
+    path_out = path_orig.with_name("out.rtdc")
+    with read.concatenated_hdf5_data(5 * [path_orig], path_out=path):
+        pass
+
+    job = logic.DCNumPipelineJob(path_in=path,
+                                 path_out=path_out,
+                                 background_kwargs={"kernel_size": 150},
+                                 basin_strategy="tap",
+                                 debug=True)
+    with logic.DCNumJobRunner(job=job) as runner:
+        runner.run()
+
+    dir_new = path_orig.parent / "another_directory"
+    dir_new.mkdir()
+    path_new = dir_new / path.name
+    path_out_new = dir_new / path_out.name
+    path.rename(path_new)
+    path_out.rename(path_out_new)
+
+    # Everything should just work, because we have relative paths in the basin.
+    with h5py.File(path_out_new) as h5:
+        assert h5.attrs["pipeline:dcnum background"] \
+               == "sparsemed:k=150^s=1^t=0^f=0.8^o=1"
+        assert "image_bg" in h5["events"]
+        assert "bg_off" in h5["events"]
+        assert "deform" in h5["events"]
+        # the rest of the original features are basins!
+        assert "time" not in h5["events"]
+        assert "image" not in h5["events"]
+        for feat in h5["events"]:
+            assert len(h5["events"][feat]) == 275
+        # The other features are accessed via basins
+        hd = read.HDF5Data(h5)
+        assert "image" in hd
+
+
 def test_chained_pipeline():
     """Test running two pipelines consecutively"""
     path_orig = retrieve_data("fmt-hdf5_cytoshot_full-features_2023.zip")