dcnum 0.25.5__py3-none-any.whl → 0.25.7__py3-none-any.whl

dcnum/meta/paths.py

@@ -1,6 +1,7 @@
 import pathlib
 
 search_path_registry = {}
+"""Dictionary keeping track of user-defined search paths"""
 
 
 def register_search_path(topic: str,

dcnum/meta/ppid.py

@@ -9,9 +9,11 @@ import warnings
 
 import numpy as np
 
-#: Increment this string if there are breaking changes that make
-#: previous pipelines unreproducible.
 DCNUM_PPID_GENERATION = "11"
+"""The dcnum pipeline generation.
+Increment this string if there are breaking changes that make
+previous pipelines unreproducible.
+"""
 
 
 class ClassWithPPIDCapabilities(Protocol):

dcnum/os_env_st.py

@@ -4,7 +4,6 @@ import os
 
 logger = logging.getLogger(__name__)
 
-#: environment variables that set number of threads
 os_env_threading = [
     "MKL_NUM_THREADS",
     "NUMBA_NUM_THREADS",
@@ -14,13 +13,14 @@ os_env_threading = [
     "OPENBLAS_NUM_THREADS",
     "VECLIB_MAXIMUM_THREADS",
 ]
+"""environment variables that define number of threads libraries will use"""
 
 
 class RequestSingleThreaded:
     """Context manager for starting a process with specific environment
 
     When entering the context, the environment variables defined in
-    `os_env_threading` are all set to "1", telling the relevant libraries
+    ``os_env_threading`` are all set to "1", telling the relevant libraries
     that they should work in single-threaded mode.
     When exiting the context, these environment variables are reset to
     their original values (or unset if applicable).

dcnum/read/cache.py

@@ -25,8 +25,10 @@ class BaseImageChunkCache(abc.ABC):
         self._dtype = None
         chunk_size = min(shape[0], chunk_size)
         self._len = self.shape[0]
-        #: This is a FILO cache for the chunks
+
         self.cache = collections.OrderedDict()
+        """This is a FILO cache for the chunks"""
+
         self.image_shape = self.shape[1:]
         self.chunk_shape = (chunk_size,) + self.shape[1:]
         self.chunk_size = chunk_size

dcnum/read/const.py

@@ -1,5 +1,3 @@
-#: Scalar features that apply to all events in a frame and which are
-#: not computed for individual events.
 PROTECTED_FEATURES = [
     "bg_off",
     "flow_rate",
@@ -10,6 +8,11 @@ PROTECTED_FEATURES = [
     "temp_amb",
     "time",
 ]
+"""Frame-defined scalar features.
+Scalar features that apply to all events in a frame and which are
+not computed for individual events
+"""
+
 
 # User-defined features may be anything, but if the user needs something
 # very specific for the pipeline, having them protected is a nice feature.

dcnum/read/detect_flicker.py

@@ -17,7 +17,7 @@ def detect_flickering(image_data: np.ndarray | HDF5Data,
     triggering signal.
 
     If flickering is detected, you should use the "sparsemed" background
-    computation with `offset_correction` set to True.
+    computation with ``offset_correction`` set to True.
 
     Parameters
     ----------

dcnum/segm/segm_torch/segm_torch_base.py

@@ -52,9 +52,10 @@ class TorchSegmenterBase(Segmenter):
         segmenter_kwargs: dict
             Keyword arguments for the segmenter
         meta: dict
-            Dictionary of metadata from an :class:`HDF5Data` instance
+            Dictionary of metadata from an :class:`.hdf5_data.HDF5Data`
+             instance
         logs: dict
-            Dictionary of logs from an :class:`HDF5Data` instance
+            Dictionary of logs from an :class:`.hdf5_data.HDF5Data` instance
 
         Returns
         -------

dcnum/segm/segm_torch/torch_postproc.py

@@ -11,6 +11,7 @@ def postprocess_masks(masks,
     """Postprocess mask images from ML segmenters
 
     The transformation includes:
+
     - Revert the cropping and padding operations done in
       :func:`.preprocess_images` by padding with zeros and cropping.
     - If the original image shape is larger than the mask image shape,

dcnum/segm/segm_torch/torch_preproc.py

@@ -11,6 +11,7 @@ def preprocess_images(images: np.ndarray,
     """Transform image data to something torch models expect
 
     The transformation includes:
+
     - normalization (division by 255, subtraction of mean, division by std)
     - cropping and padding of the input images to `image_shape`. For padding,
       the median of each *individual* image is used.

dcnum/segm/segmenter.py

@@ -26,17 +26,23 @@ class SegmenterNotApplicableError(BaseException):
 
 
 class Segmenter(abc.ABC):
-    #: Required hardware ("cpu" or "gpu") defined in first-level subclass.
     hardware_processor = "none"
-    #: Whether to enable mask post-processing. If disabled, you should
-    #: make sure that your mask is properly defined and cleaned or you
-    #: have to call `process_mask` in your `segment_algorithm` implementation.
+    """Required hardware ("cpu" or "gpu") defined in first-level subclass."""
+
     mask_postprocessing = True
-    #: Default keyword arguments for mask post-processing. See `process_mask`
-    #: for available options.
+    """Whether to enable mask post-processing.
+    If disabled, you should make sure that your mask is properly defined
+    and cleaned or you have to call `process_mask` in your
+    ``segment_algorithm`` implementation.
+    """
+
     mask_default_kwargs = {}
-    #: If the segmenter requires a background-corrected image, set this to True
+    """Default keyword arguments for mask post-processing.
+    See `process_mask` for available options.
+    """
+
     requires_background_correction = False
+    """Whether the segmenter requires a background-corrected image"""
 
     def __init__(self,
                  *,
@@ -46,10 +52,11 @@ class Segmenter(abc.ABC):
         """Base segmenter class
 
         This is the base segmenter class for the multiprocessing operation
-        segmenter :class:`.MPOSegmenter` (multiple subprocesses are spawned
-        and each of them works on a queue of images) and the single-threaded
-        operation segmenter :class:`.STOSegmenter` (e.g. for batch
-        segmentation on a GPU).
+        segmenter :class:`.segmenter_mpo.MPOSegmenter` (multiple
+        subprocesses are spawned and each of them works on a queue of images)
+        and the single-threaded operation segmenter
+        :class:`.segmenter_sto.STOSegmenter` (e.g. for batch segmentation on
+        a GPU).
 
         Parameters
         ----------
@@ -64,12 +71,15 @@ class Segmenter(abc.ABC):
         self.logger = logging.getLogger(__name__).getChild(
             self.__class__.__name__)
         spec = inspect.getfullargspec(self.segment_algorithm)
-        #: custom keyword arguments for the subclassing segmenter
+
         self.kwargs = spec.kwonlydefaults or {}
+        """custom keyword arguments for the subclassing segmenter"""
+
         self.kwargs.update(kwargs)
 
-        #: keyword arguments for mask post-processing
         self.kwargs_mask = {}
+        """keyword arguments for mask post-processing"""
+
         if self.mask_postprocessing:
             spec_mask = inspect.getfullargspec(self.process_mask)
             self.kwargs_mask.update(spec_mask.kwonlydefaults or {})
@@ -108,7 +118,7 @@ class Segmenter(abc.ABC):
             KEY:KW_APPROACH:KW_MASK
 
         Where KEY is e.g. "legacy" or "watershed", and KW_APPROACH is a
-        list of keyword arguments for `segment_algorithm`, e.g.::
+        list of keyword arguments for ``segment_algorithm``, e.g.::
 
             thresh=-6^blur=0
 
@@ -296,10 +306,10 @@ class Segmenter(abc.ABC):
 
     @functools.cache
     def segment_algorithm_wrapper(self):
-        """Wraps `self.segment_algorithm` to only accept an image
+        """Wraps ``self.segment_algorithm`` to only accept an image
 
-        The static method `self.segment_algorithm` may optionally accept
-        keyword arguments `self.kwargs`. This wrapper returns the
+        The static method ``self.segment_algorithm`` may optionally accept
+        keyword arguments ``self.kwargs``. This wrapper returns the
         wrapped method that only accepts the image as an argument. This
         makes sense if you want to unify
         """
@@ -336,7 +346,7 @@ class Segmenter(abc.ABC):
             additional background offset values that should be subtracted
             from the image data before segmentation. Should only be
             used in combination with segmenters that have
-            `requires_background_correction` set to True.
+            ``requires_background_correction`` set to True.
         """
         images = image_data.get_chunk(chunk)
         if bg_off is not None:
@@ -364,9 +374,10 @@ class Segmenter(abc.ABC):
         segmenter_kwargs: dict
             Keyword arguments for the segmenter
         meta: dict
-            Dictionary of metadata from an :class:`HDF5Data` instance
+            Dictionary of metadata from an :class:`.hdf5_data.HDF5Data`
+            instance
         logs: dict
-            Dictionary of logs from an :class:`HDF5Data` instance
+            Dictionary of logs from an :class:`.hdf5_data.HDF5Data` instance
 
         Returns
         -------

dcnum/segm/segmenter_manager_thread.py

@@ -36,8 +36,8 @@ class SegmenterManagerThread(threading.Thread):
             its job for a slot, the slot value will be set to "e" (for
             "task is with feature extractor").
         slot_chunks:
-            For each slot in `slot_states`, this shared array defines
-            on which chunk in `image_data` the segmentation took place.
+            For each slot in ``slot_states``, this shared array defines
+            on which chunk in ``image_data`` the segmentation took place.
         bg_off:
             1d array containing additional background image offset values
             that are added to each background image before subtraction
@@ -45,10 +45,10 @@ class SegmenterManagerThread(threading.Thread):
 
         Notes
         -----
-        This manager keeps a list `labels_list` which enumerates the
-        slots just like `slot_states` and `slot_chunks` do. For each
+        This manager keeps a list ``labels_list`` which enumerates the
+        slots just like ``slot_states` and ``slot_chunks`` do. For each
         slot, this list contains the labeled image data (integer-valued)
-        for the input `image_data` chunks.
+        for the input ``image_data`` chunks.
 
         The working principle of this `SegmenterManagerThread` allows
         the user to define a fixed number of slots on which the segmenter
@@ -61,21 +61,28 @@ class SegmenterManagerThread(threading.Thread):
         super(SegmenterManagerThread, self).__init__(
               name="SegmenterManager", *args, **kwargs)
         self.logger = logging.getLogger("dcnum.segm.SegmenterManagerThread")
-        #: Segmenter instance
+
         self.segmenter = segmenter
-        #: Image data which is being segmented
+        """Segmenter instance"""
+
         self.image_data = image_data
-        #: Additional, optional background offset
+        """Image data which is being segmented"""
+
         self.bg_off = (
             bg_off if self.segmenter.requires_background_correction else None)
-        #: Slot states
+        """Additional, optional background offset"""
+
         self.slot_states = slot_states
-        #: Current slot chunk index for the slot states
+        """Slot states"""
+
         self.slot_chunks = slot_chunks
-        #: List containing the segmented labels of each slot
+        """Current slot chunk index for the slot states"""
+
         self.labels_list = [None] * len(self.slot_states)
-        #: Time counter for segmentation
+        """List containing the segmented labels of each slot"""
+
         self.t_count = 0
+        """Time counter for segmentation"""
 
     def run(self):
         num_slots = len(self.slot_states)

dcnum/segm/segmenter_mpo.py

@@ -35,7 +35,7 @@ class MPOSegmenter(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.
         """
         super(MPOSegmenter, self).__init__(kwargs_mask=kwargs_mask,
@@ -145,7 +145,7 @@ class MPOSegmenter(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
@@ -264,7 +264,7 @@ class MPOSegmenter(Segmenter, abc.ABC):
         """Return the integer label image for an input image
 
         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.
         """
         segm_wrap = self.segment_algorithm_wrapper()
@@ -296,7 +296,7 @@ class MPOSegmenterWorker:
 
         Parameters
         ----------
-        segmenter: MPOSegmenter
+        segmenter: .segmenter_mpo.MPOSegmenter
             The segmentation instance
         sl_start: int
             Start of slice of input array to process

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-0.25.5.dist-info → dcnum-0.25.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: dcnum
-Version: 0.25.5
+Version: 0.25.7
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller, Raghava Alajangi
 Maintainer-email: Paul Müller <dev@craban.de>

dcnum-0.25.7.dist-info/RECORD

@@ -0,0 +1,57 @@
+dcnum/__init__.py,sha256=hcawIKS7utYiOyVhOAX9t7K3xYzP1b9862VV0b6qSrQ,74
+dcnum/_version.py,sha256=hjm1pvHN0ZX7nlIod7PG7Fba0cyr_wIaCY9stsERSag,513
+dcnum/os_env_st.py,sha256=4psq-gPuWTTQ118kCiTx0Mhoyads4Irn6JSUzZk8gyc,3052
+dcnum/feat/__init__.py,sha256=jUJYWTD3VIoDNKrmryXbjHb1rGwYtK4b7VPWihYgUoo,325
+dcnum/feat/event_extractor_manager_thread.py,sha256=6D3RVYBuH7gOoGZ4Kz74n6fhq7MtlTY26kpSwZRqg3M,7972
+dcnum/feat/gate.py,sha256=EOleB83sOlBjc8bjaZfWwGuxfCcEO5mknuFunlw_j7o,7252
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+dcnum/feat/feat_contour/__init__.py,sha256=Td4Hs47kUgJj0VXm3q5ofXhaUWr9QTfVgbwh5EELA-I,163
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+dcnum/logic/ctrl.py,sha256=c06ZOUD0T4_FdQDHbigkLAPQTyoeFxhETg-K3W1UyeM,37520
+dcnum/logic/job.py,sha256=MprDL6DwXWmvtGgy7W9A7s2rVRx68ObdJB8mvGFwVcw,7718
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+dcnum/meta/ppid.py,sha256=JInGtwSCsO9nr1E1aishm0k9iQIFB-essBKvv5aBE98,8510
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{dcnum-0.25.5.dist-info → dcnum-0.25.7.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (76.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

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