dcnum 0.25.6__py3-none-any.whl → 0.25.8__py3-none-any.whl

dcnum/segm/segmenter_sto.py

@@ -27,7 +27,7 @@ class STOSegmenter(Segmenter, abc.ABC):
         debug: bool
             Debugging parameters
         kwargs:
-            Additional, optional keyword arguments for `segment_algorithm`
+            Additional, optional keyword arguments for ``segment_algorithm``
             defined in the subclass.
         """
         if num_workers not in [None, 1]:
@@ -46,7 +46,7 @@ class STOSegmenter(Segmenter, abc.ABC):
         """Perform batch segmentation of `images`
 
         Before segmentation, an optional background offset correction with
-        `bg_off` is performed. After segmentation, mask postprocessing is
+        ``bg_off`` is performed. After segmentation, mask postprocessing is
         performed according to the class definition.
 
         Parameters

dcnum/write/queue_collector_thread.py

@@ -26,23 +26,31 @@ class EventStash:
             List that defines how many events there are for each input
             frame. If summed up, this defines `self.size`.
         """
-        #: Dictionary containing the event arrays
         self.events = {}
-        #: List containing the number of events per input frame
+        """Dictionary containing the event arrays"""
+
         self.feat_nevents = feat_nevents
-        #: Cumulative sum of `feat_nevents` for determining sorting offsets
+        """List containing the number of events per input frame"""
+
         self.nev_idx = np.cumsum(feat_nevents)
-        #: Number of events in this stash
+        """Cumulative sum of `feat_nevents` for determining sorting offsets"""
+
         self.size = int(np.sum(feat_nevents))
-        #: Number of frames in this stash
+        """Number of events in this stash"""
+
         self.num_frames = len(feat_nevents)
-        #: Global offset compared to the original data instance.
+        """Number of frames in this stash"""
+
         self.index_offset = index_offset
-        #: Array containing the indices in the original data instance
-        #: that correspond to the events in `events`.
+        """Global offset compared to the original data instance."""
+
         self.indices_for_data = np.zeros(self.size, dtype=np.uint32)
-        # Private array that tracks the progress.
+        """Array containing the indices in the original data instance.
+        These indices correspond to the events in `events`.
+        """
+
         self._tracker = np.zeros(self.num_frames, dtype=bool)
+        """Private array that tracks the progress."""
 
     def is_complete(self):
         """Determine whether the event stash is complete (all events added)"""
@@ -141,22 +149,31 @@ class QueueCollectorThread(threading.Thread):
         super(QueueCollectorThread, self).__init__(
               name="QueueCollector", *args, **kwargs)
         self.logger = logging.getLogger("dcnum.write.QueueCollector")
-        #: Event queue from which to collect event data
+
         self.event_queue = event_queue
-        #: Writer deque to which event arrays are appended
+        """Event queue from which to collect event data"""
+
         self.writer_dq = writer_dq
-        #: Buffer deque to which events are appended that do not belong
-        #: to the current chunk (chunk defined by `write_threshold`).
+        """Writer deque to which event arrays are appended"""
+
         self.buffer_dq = deque()
-        #: A shared array containing the number of events for each
-        #: frame in `data`.
+        """Buffer deque
+        Events that do not not belong to the current chunk
+        (chunk defined by `write_threshold`) go here.
+        """
+
         self.feat_nevents = feat_nevents
-        #: Number of frames to send to `writer_dq` at a time.
+        """shared array containing the number of events
+        for each frame in `data`."""
+
         self.write_threshold = write_threshold
-        #: Number of events sent to `writer_dq`
+        """Number of frames to send to `writer_dq` at a time."""
+
         self.written_events = 0
-        #: Number of frames from `data` written to `writer_dq`
+        """Number of events sent to `writer_dq`"""
+
         self.written_frames = 0
+        """Number of frames from `data` written to `writer_dq`"""
 
     def run(self):
         # We are not writing to `event_queue` so we can safely cancel

dcnum/write/writer.py

@@ -275,13 +275,13 @@ class HDF5Writer:
     def store_log(self,
                   log: str,
                   data: List[str],
-                  override: bool = False):
+                  override: bool = False) -> h5py.Dataset:
         """Store log data
 
         Store the log data under the key `log`. The `data`
         kwarg must be a list of strings. If the log entry
         already exists, `ValueError` is raised unless
-        `override` is set to True.
+        ``override`` is set to True.
         """
         logs = self.h5.require_group("logs")
         if log in logs:
@@ -290,7 +290,7 @@ class HDF5Writer:
             else:
                 raise ValueError(
                     f"Log '{log}' already exists in {self.h5.filename}!")
-        logs.create_dataset(
+        log_ds = logs.create_dataset(
             name=log,
             data=data,
             shape=(len(data),),
@@ -298,6 +298,7 @@ class HDF5Writer:
             dtype=f"S{max([len(ll) for ll in data])}",
             chunks=True,
             **self.ds_kwds)
+        return log_ds
 
 
 def create_with_basins(

{dcnum-0.25.6.dist-info → dcnum-0.25.8.dist-info}/METADATA

@@ -1,10 +1,10 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: dcnum
-Version: 0.25.6
+Version: 0.25.8
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller, Raghava Alajangi
 Maintainer-email: Paul Müller <dev@craban.de>
-License: MIT
+License-Expression: MIT
 Project-URL: source, https://github.com/DC-Analysis/dcnum
 Project-URL: tracker, https://github.com/DC-Analysis/dcnum/issues
 Project-URL: documentation, https://dcnum.readthedocs.io/en/stable/
@@ -27,6 +27,7 @@ Requires-Dist: scikit-image<1,>=0.24
 Requires-Dist: scipy<1.15.0,>=1.8.0
 Provides-Extra: torch
 Requires-Dist: torch>=2.2; extra == "torch"
+Dynamic: license-file
 
 |dcnum|
 =======

dcnum-0.25.8.dist-info/RECORD

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{dcnum-0.25.6.dist-info → dcnum-0.25.8.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (78.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{dcnum-0.25.6.dist-info → dcnum-0.25.8.dist-info/licenses}/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023 Deformability Cytometry Analysis
+Copyright (c) 2023 Paul Müller
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

dcnum-0.25.6.dist-info/RECORD

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