dcnum 0.20.1__tar.gz → 0.20.3__tar.gz

{dcnum-0.20.1 → dcnum-0.20.3}/CHANGELOG

@@ -1,3 +1,7 @@
+0.20.3
+ - enh: improve strategy for stalling for slow writer
+0.20.2
+ - ref: remove __init__ from SegmentThresh
 0.20.1
  - fix: relative basin locations not written correctly
  - enh: increase deque size threshold for waiting for writer

{dcnum-0.20.1/src/dcnum.egg-info → dcnum-0.20.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.20.1
+Version: 0.20.3
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.20.1 → dcnum-0.20.3}/src/dcnum/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.20.1'
-__version_tuple__ = version_tuple = (0, 20, 1)
+__version__ = version = '0.20.3'
+__version_tuple__ = version_tuple = (0, 20, 3)

{dcnum-0.20.1 → dcnum-0.20.3}/src/dcnum/feat/event_extractor_manager_thread.py

@@ -95,12 +95,14 @@ class EventExtractorManagerThread(threading.Thread):
         while True:
             # 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 > 1000:
-                stallsec = ldq / 1000
+            if (ldq := len(self.writer_dq)) > 1000:
+                time.sleep(1)
+                ldq2 = len(self.writer_dq)
+                stall_time = (ldq2 - 200) / (ldq - ldq2) if ldq2 > 200 else 0
+                time.sleep(stall_time)
                 self.logger.warning(
-                    f"Stalling {stallsec:.1f}s for slow writer")
-                time.sleep(stallsec)
+                    f"Stalled {stall_time + 1:.1f}s for slow writer "
+                    f"({ldq} chunks queued)")
 
             cur_slot = 0
             unavailable_slots = 0

{dcnum-0.20.1 → dcnum-0.20.3}/src/dcnum/logic/ctrl.py

@@ -666,7 +666,6 @@ class DCNumJobRunner(threading.Thread):
         num_extractors = max(1, num_extractors)
         num_segmenters = max(1, num_segmenters)
         self.job.kwargs["segmenter_kwargs"]["num_workers"] = num_segmenters
-
         slot_chunks = mp_spawn.Array("i", num_slots)
         slot_states = mp_spawn.Array("u", num_slots)
 

{dcnum-0.20.1 → dcnum-0.20.3}/src/dcnum/segm/segm_thresh.py

@@ -10,18 +10,6 @@ class SegmentThresh(CPUSegmenter):
     }
     requires_background_correction = True
 
-    def __init__(self, thresh=-6, *args, **kwargs):
-        """Simple image thresholding segmentation
-
-        Parameters
-        ----------
-        thresh: int
-            grayscale threshold value for creating the mask image;
-            For a background-corrected image, pixels with values below
-            this value are considered to be part of the mask.
-        """
-        super(SegmentThresh, self).__init__(thresh=thresh, *args, **kwargs)
-
     @staticmethod
     def segment_approach(image, *,
                          thresh: float = -6):

{dcnum-0.20.1 → dcnum-0.20.3/src/dcnum.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.20.1
+Version: 0.20.3
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.20.1 → dcnum-0.20.3}/tests/test_meta_ppid_segm.py

@@ -1,3 +1,4 @@
+from dcnum.meta import ppid
 from dcnum import segm
 
 import pytest
@@ -26,6 +27,22 @@ def test_ppid_decoding_thresh_check_kwargs():
     assert kwargs["kwargs_mask"]["closing_disk"] == 3
 
 
+def test_ppid_kwargs_to_ppid():
+    """Make sure that subclasses correctly implement __init__ (if they do)"""
+    segm_dict = segm.get_available_segmenters()
+    for segm_key in segm_dict:
+        segm_cls = segm_dict[segm_key]
+        inst = segm_cls()
+        kwargs = inst.kwargs
+        kwargs["num_workers"] = 2
+        ppid.kwargs_to_ppid(
+            cls=segm_cls,
+            method="segment_approach",
+            kwargs=kwargs,
+            allow_invalid_keys=False,
+        )
+
+
 @pytest.mark.parametrize("segm_code", segm.get_available_segmenters().keys())
 def test_ppid_required_method_definitions(segm_code):
     segm_class = segm.get_available_segmenters()[segm_code]