dcnum 0.20.0__tar.gz → 0.20.2__tar.gz

{dcnum-0.20.0 → dcnum-0.20.2}/CHANGELOG

@@ -1,3 +1,8 @@
+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
 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-0.20.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.20.0
+Version: 0.20.2
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.20.0 → dcnum-0.20.2}/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 = '0.20.2'
+__version_tuple__ = version_tuple = (0, 20, 2)

{dcnum-0.20.0 → dcnum-0.20.2}/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-0.20.2}/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,
@@ -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-0.20.0 → dcnum-0.20.2}/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-0.20.2}/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-0.20.0 → dcnum-0.20.2/src/dcnum.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.20.0
+Version: 0.20.2
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.20.0 → dcnum-0.20.2}/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")

{dcnum-0.20.0 → dcnum-0.20.2}/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]