dcnum 0.16.8__tar.gz → 0.17.1__tar.gz

{dcnum-0.16.8 → dcnum-0.17.1}/CHANGELOG

@@ -1,3 +1,16 @@
+0.17.1
+ - ref: remove "bg_med" and "index_online" from protected scalar features,
+   because "bg_med" may change due to a different background computation
+   method and "index_online" enumerates events from online segmentation
+0.17.0
+ - feat: allow to register topical search paths
+ - ref: remove deprecated `get_ppid_from_kwargs` methods
+ - ref: remove deprecated `preselect` and `ptp_median` keyword
+   arguments from `QueueEventExtractor`
+ - ref: remove deprecated "key" from `get_class_method_info` info dict
+ - ref: issue UserWarning instead of DeprecationWarning when
+ - ref: remove pixel size check for HDF5 data
+ - ref: remove unused `_get_model_file` from GPUSegmenter
 0.16.8
  - fix: correctly set number of workers for CPUSegmenter
  - enh: update list of environment variables that should be set to

{dcnum-0.16.8 → dcnum-0.17.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.16.8
+Version: 0.17.1
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.16.8 → dcnum-0.17.1}/src/dcnum/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.16.8'
-__version_tuple__ = version_tuple = (0, 16, 8)
+__version__ = version = '0.17.1'
+__version_tuple__ = version_tuple = (0, 17, 1)

{dcnum-0.16.8 → dcnum-0.17.1}/src/dcnum/feat/feat_background/base.py

@@ -4,7 +4,6 @@ import inspect
 import multiprocessing as mp
 import pathlib
 import uuid
-import warnings
 
 import h5py
 import numpy as np
@@ -212,13 +211,6 @@ class Background(abc.ABC):
     def process_approach(self):
         """The actual background computation approach"""
 
-    @classmethod
-    def get_ppid_from_kwargs(cls, kwargs):
-        warnings.warn(
-            "Please use get_ppid_from_ppkw instead of get_ppid_from_kwargs",
-            DeprecationWarning)
-        return cls.get_ppid_from_ppkw(kwargs)
-
 
 @functools.cache
 def get_available_background_methods():

{dcnum-0.16.8 → dcnum-0.17.1}/src/dcnum/feat/gate.py

@@ -139,13 +139,6 @@ class Gate:
                                 ppid=pp_gate_kwargs)
         return kwargs
 
-    @classmethod
-    def get_ppid_from_kwargs(cls, kwargs):
-        warnings.warn(
-            "Please use get_ppid_from_ppkw instead of get_ppid_from_kwargs",
-            DeprecationWarning)
-        return cls.get_ppid_from_ppkw(kwargs)
-
     def gate_event(self, event):
         """Return None if the event should not be used, else `event`"""
         if self.box_gates and event:

{dcnum-0.16.8 → dcnum-0.17.1}/src/dcnum/feat/queue_event_extractor.py

@@ -7,7 +7,6 @@ import os
 import queue
 import threading
 import traceback
-import warnings
 
 import numpy as np
 
@@ -126,8 +125,7 @@ class QueueEventExtractor:
                         num_extractors: int,
                         log_queue: mp.Queue,
                         log_level: int = logging.INFO,
-                        preselect: None = None,
-                        ptp_median: None = None):
+                        ):
         """Get initialization arguments for :cass:`.QueueEventExtractor`
 
         This method was created for convenience reasons:
@@ -147,8 +145,6 @@ class QueueEventExtractor:
             Queue the worker uses for sending log messages
         log_level: int
             Logging level to use in the worker process
-        preselect, ptp_median:
-            Deprecated
 
         Returns
         -------
@@ -160,13 +156,6 @@ class QueueEventExtractor:
         # queue with event-wise feature dictionaries
         event_queue = mp_spawn.Queue()
 
-        if preselect is not None:
-            warnings.warn("The `preselect` argument is deprecated!",
-                          DeprecationWarning)
-        if ptp_median is not None:
-            warnings.warn("The `ptp_median` argument is deprecated!",
-                          DeprecationWarning)
-
         # Note that the order must be identical to  __init__
         args = collections.OrderedDict()
         args["data"] = data
@@ -382,13 +371,6 @@ class QueueEventExtractor:
             self.log_queue.close()
             self.log_queue.join_thread()
 
-    @classmethod
-    def get_ppid_from_kwargs(cls, kwargs):
-        warnings.warn(
-            "Please use get_ppid_from_ppkw instead of get_ppid_from_kwargs",
-            DeprecationWarning)
-        return cls.get_ppid_from_ppkw(kwargs)
-
 
 class EventExtractorProcess(QueueEventExtractor, mp_spawn.Process):
     """Multiprocessing worker for regular segmentation and extraction"""

{dcnum-0.16.8 → dcnum-0.17.1}/src/dcnum/meta/__init__.py

@@ -1,2 +1,3 @@
 # flake8: noqa: F401
+from . import paths
 from . import ppid

dcnum-0.17.1/src/dcnum/meta/paths.py

@@ -0,0 +1,30 @@
+import pathlib
+
+search_path_registry = {}
+
+
+def register_search_path(topic: str,
+                         search_path: str | pathlib.Path):
+    """Register a search path for a given topic
+
+    Search paths are a global solution for organizing the locations
+    of resources that are part of an analysis pipeline. For instance,
+    if the location of such a file that depends on where your pipeline is
+    running, you can register multiple search paths and the file will
+    be found using :func:`find_file`.
+    """
+    topic_list = search_path_registry.setdefault(topic, [])
+    topic_list.append(pathlib.Path(search_path))
+
+
+def find_file(topic: str,
+              file_name: str):
+    """Find a file in the search path for the given topic"""
+    search_paths = search_path_registry.get(topic, [])
+    for pp in search_paths:
+        pf = pp / file_name
+        if pf.is_file():
+            return pf
+    else:
+        raise KeyError(f"Could not find {file_name} for {topic} in the "
+                       f"registered search paths {search_paths}")

{dcnum-0.16.8 → dcnum-0.17.1}/src/dcnum/meta/ppid.py

@@ -71,14 +71,8 @@ def get_class_method_info(class_obj: ClassWithPPIDCapabilities,
         are extracted.
     """
     doc = class_obj.__doc__ or class_obj.__init__.__doc__
-    if hasattr(class_obj, "key"):
-        warnings.warn(f"{class_obj.__class__} implements `key` which is "
-                      f"deprecated. Please rename to `get_ppid_code`.",
-                      DeprecationWarning)
-        setattr(class_obj, "get_ppid_code", class_obj.key)
     info = {
         "code": class_obj.get_ppid_code(),
-        "key": class_obj.get_ppid_code(),  # Deprecated
         "doc": doc,
         "title": doc.split("\n")[0],
         }
@@ -116,11 +110,10 @@ def kwargs_to_ppid(cls: ClassWithPPIDCapabilities,
                    f"segmenter and had to implement `__init__`, make sure "
                    f"that it accepts all kwonly-arguments its super class "
                    f"accepts. If this is not the case, you are probably "
-                   f"passing bad kwargs to the segmenter!"
+                   f"passing invalid kwargs to the segmenter."
                    )
             if allow_invalid_keys:
-                warnings.warn(msg + " Please cleanup your code!",
-                              DeprecationWarning)
+                warnings.warn(msg, UserWarning)
             else:
                 raise KeyError(msg)
         kwannot = info["annotations"][method]

{dcnum-0.16.8 → dcnum-0.17.1}/src/dcnum/read/const.py

@@ -1,10 +1,9 @@
-#: Scalar features that apply to all events in a frame
+#: Scalar features that apply to all events in a frame and which are
+#: not computed from image or image_bg data.
 PROTECTED_FEATURES = [
-    "bg_med",
     "flow_rate",
     "frame",
     "g_force",
-    "index_online",
     "pressure",
     "temp",
     "temp_amb",

{dcnum-0.16.8 → dcnum-0.17.1}/src/dcnum/read/hdf5_data.py

@@ -162,20 +162,6 @@ class HDF5Data:
 
         if state["pixel_size"] is not None:
             self.pixel_size = state["pixel_size"]
-        else:
-            # Set known pixel size if possible
-            did = self.meta.get("setup:identifier", "EMPTY")
-            if (did.startswith("RC-")
-                    and (self.pixel_size < 0.255 or self.pixel_size > 0.275)):
-                warnings.warn(
-                    f"Correcting for invalid pixel size in '{self.path}'!")
-                warnings.warn(
-                    "Correcting the pixel size is deprecated in dcnum; please "
-                    "make sure your input data are clean before processing",
-                    DeprecationWarning
-                )
-                # Set default pixel size for Rivercyte devices
-                self.pixel_size = 0.2645
 
         self.image_cache_size = state["image_cache_size"]
 

{dcnum-0.16.8 → dcnum-0.17.1}/src/dcnum/segm/segm_thresh.py

@@ -15,6 +15,10 @@ class SegmentThresh(CPUSegmenter):
 
         Parameters
         ----------
+        thresh: int
+            grayscale threhold 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)
 

{dcnum-0.16.8 → dcnum-0.17.1}/src/dcnum/segm/segmenter.py

@@ -4,7 +4,6 @@ import functools
 import inspect
 import logging
 from typing import Dict
-import warnings
 
 import cv2
 import numpy as np
@@ -132,10 +131,10 @@ class Segmenter(abc.ABC):
         # Start with the default mask kwargs defined for this subclass
         kwargs_mask_used = copy.deepcopy(cls.mask_default_kwargs)
         kwargs_mask_used.update(kwargs_mask)
-        key = cls.get_ppid_code()
+        code = cls.get_ppid_code()
         csegm = kwargs_to_ppid(cls, "segment_approach", kwargs)
         cmask = kwargs_to_ppid(cls, "process_mask", kwargs_mask_used)
-        return ":".join([key, csegm, cmask])
+        return ":".join([code, csegm, cmask])
 
     @staticmethod
     def get_ppkw_from_ppid(segm_ppid):
@@ -280,13 +279,6 @@ class Segmenter(abc.ABC):
     def segment_batch(self, data, start=None, stop=None):
         """Return the integer labels for an entire batch"""
 
-    @classmethod
-    def get_ppid_from_kwargs(cls, *args, **kwargs):
-        warnings.warn(
-            "Please use get_ppid_from_ppkw instead of get_ppid_from_kwargs.",
-            DeprecationWarning)
-        return cls.get_ppid_from_ppkw(*args, **kwargs)
-
 
 @functools.cache
 def get_available_segmenters():

{dcnum-0.16.8 → dcnum-0.17.1}/src/dcnum/segm/segmenter_gpu.py

@@ -1,5 +1,4 @@
 import abc
-import pathlib
 from typing import Dict
 
 import numpy as np
@@ -39,11 +38,6 @@ class GPUSegmenter(Segmenter, abc.ABC):
                                            debug=debug,
                                            **kwargs)
 
-    @staticmethod
-    def _get_model_path(model_file):
-        """Custom hook that may be defined by subclasses"""
-        return pathlib.Path(model_file)
-
     def segment_batch(self,
                       image_data: np.ndarray,
                       start: int = None,

{dcnum-0.16.8 → dcnum-0.17.1}/src/dcnum.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.16.8
+Version: 0.17.1
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.16.8 → dcnum-0.17.1}/src/dcnum.egg-info/SOURCES.txt

@@ -40,6 +40,7 @@ src/dcnum/logic/ctrl.py
 src/dcnum/logic/job.py
 src/dcnum/logic/json_encoder.py
 src/dcnum/meta/__init__.py
+src/dcnum/meta/paths.py
 src/dcnum/meta/ppid.py
 src/dcnum/read/__init__.py
 src/dcnum/read/cache.py
@@ -73,17 +74,18 @@ tests/test_logic_job.py
 tests/test_logic_join.py
 tests/test_logic_json.py
 tests/test_logic_pipeline.py
-tests/test_ppid.py
-tests/test_ppid_bg.py
-tests/test_ppid_data.py
-tests/test_ppid_feat.py
-tests/test_ppid_gate.py
-tests/test_ppid_segm.py
+tests/test_meta_paths.py
+tests/test_meta_ppid_base.py
+tests/test_meta_ppid_bg.py
+tests/test_meta_ppid_data.py
+tests/test_meta_ppid_feat.py
+tests/test_meta_ppid_gate.py
+tests/test_meta_ppid_segm.py
 tests/test_read_basin.py
 tests/test_read_concat_hdf5.py
 tests/test_read_hdf5.py
+tests/test_segm_base.py
 tests/test_segm_thresh.py
-tests/test_segmenter.py
 tests/test_write_deque_writer_thread.py
 tests/test_write_queue_collector_thread.py
 tests/test_write_writer.py

dcnum-0.17.1/tests/test_meta_paths.py

@@ -0,0 +1,42 @@
+import pytest
+
+from dcnum.meta import paths
+
+
+@pytest.fixture(autouse=True)
+def clear_search_paths():
+    paths.search_path_registry.clear()
+
+
+def test_find_file_in_path(tmp_path):
+    file = tmp_path / "myfile.txt"
+    file.touch()
+    # register a search path
+    paths.register_search_path("hans", tmp_path)
+    act = paths.find_file("hans", file.name)
+    assert str(act.resolve()) == str(file.resolve())
+
+
+def test_find_file_in_path_multiple(tmp_path):
+    dir1 = tmp_path / "foo"
+    dir2 = tmp_path / "bar"
+    file = dir2 / "myfile.txt"
+    dir1.mkdir()
+    dir2.mkdir()
+    file.touch()
+    # register a search path
+    paths.register_search_path("mantra", dir1)
+    paths.register_search_path("mantra", dir2)
+    act = paths.find_file("mantra", file.name)
+    assert str(act.resolve()) == str(file.resolve())
+
+
+def test_find_file_in_path_not_found(tmp_path):
+    # find non-existent file
+    with pytest.raises(KeyError, match="Could not find"):
+        paths.find_file("peter", "myfile.txt")
+
+    # register a search path
+    paths.register_search_path("hans", tmp_path / "does_not_exist")
+    with pytest.raises(KeyError, match="Could not find"):
+        paths.find_file("hans", "myfile.txt")

{dcnum-0.16.8 → dcnum-0.17.1}/tests/test_read_hdf5.py

@@ -201,7 +201,10 @@ def test_open_real_data():
 
         # scalar features
         fsc = h5dat.features_scalar_frame
-        exp = ['bg_med', 'frame', 'time']
+        # Changed in version 0.17.1: bg_med is not returned anymore,
+        # because it is computed from the background image which
+        # depends on the background method employed.
+        exp = ['frame', 'time']
         assert set(fsc) == set(exp)
 
         # feature names