dcnum 0.11.4__py3-none-any.whl → 0.11.6__py3-none-any.whl

dcnum/_version.py

@@ -1,4 +1,4 @@
 # file generated by setuptools_scm
 # don't change, don't track in version control
-__version__ = version = '0.11.4'
-__version_tuple__ = version_tuple = (0, 11, 4)
+__version__ = version = '0.11.6'
+__version_tuple__ = version_tuple = (0, 11, 6)

dcnum/feat/queue_event_extractor.py

@@ -257,7 +257,21 @@ class QueueEventExtractor:
                 if self.finalize_extraction.value:
                     # The manager told us that there is nothing more coming.
                     self.logger.debug(
-                        f"Finalizing worker {self} with PID {os.getpid()}")
+                        f"Finalizing worker {self} with PID {os.getpid()}. "
+                        f"{self.event_queue.qsize()} events are still queued.")
+                    # Tell the queue background thread to flush all data to
+                    # the queue. The background thread will quit once it has
+                    # flushed all buffered data to the pipe.
+                    self.event_queue.close()
+                    self.logger.debug(
+                        f"Closed event queue from Process PID {os.getpid()}")
+                    # Join the queue background thread. It blocks until the
+                    # background thread exits, ensuring that all data in the
+                    # buffer has been flushed to the pipe.
+                    self.event_queue.join_thread()
+                    self.logger.debug(
+                        f"Joined event queue background thread from"
+                        f"Process PID {os.getpid()}")
                     break
             else:
                 try:

dcnum/write/queue_collector_thread.py

@@ -183,12 +183,14 @@ class QueueCollectorThread(threading.Thread):
                 continue
 
             if len(cur_nevents) == 0:
-                self.logger.warning("Encountered empty nevents array!")
+                self.logger.info(
+                    "Reached the end of the current dataset (frame "
+                    f"{cur_frame + 1} of {len(self.feat_nevents)}).")
                 break
 
             # We have reached the writer threshold. This means the extractor
             # has analyzed at least `write_threshold` frames (not events).
-            self.logger.debug(f"Current frane: {cur_frame}")
+            self.logger.debug(f"Current frame: {cur_frame}")
 
             # Create an event stash
             stash = EventStash(
@@ -214,6 +216,7 @@ class QueueCollectorThread(threading.Thread):
                 try:
                     idx, events = self.event_queue.get(timeout=.3)
                 except queue.Empty:
+                    # No time.sleep here, because we are using timeout above.
                     continue
                 if cur_frame <= idx < cur_frame + self.write_threshold:
                     stash.add_events(index=idx, events=events)
@@ -253,6 +256,8 @@ class QueueCollectorThread(threading.Thread):
 
             # Write the number of events.
             self.writer_dq.append(("nevents",
+                                   # Get nevents for each event from the
+                                   # frame-based cur_nevents array.
                                    np.array(stash.feat_nevents)[
                                        indices - stash.index_offset]
                                    ))
@@ -261,4 +266,4 @@ class QueueCollectorThread(threading.Thread):
             self.written_frames += stash.num_frames
 
             # Increment current frame index.
-            cur_frame += self.write_threshold
+            cur_frame += len(cur_nevents)

{dcnum-0.11.4.dist-info → dcnum-0.11.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.11.4
+Version: 0.11.6
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Paul Müller
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.11.4.dist-info → dcnum-0.11.6.dist-info}/RECORD

@@ -1,9 +1,9 @@
 dcnum/__init__.py,sha256=hcawIKS7utYiOyVhOAX9t7K3xYzP1b9862VV0b6qSrQ,74
-dcnum/_version.py,sha256=Bbplzvuz1KWstfyKIRofOtvOUu7akc5l3tJGqDcI0-E,162
+dcnum/_version.py,sha256=3Gew5At6W5w-3RNIQtvr0brz3P-MJACFL9J-IorkINc,162
 dcnum/feat/__init__.py,sha256=0oX765AyfL1BcVt-FI6R_i6x5LgYYLeyO5lkxSauI0Y,299
 dcnum/feat/event_extractor_manager_thread.py,sha256=54eCKbLBkv3U7RLGfqtiMB1CnqHNKcTm9vJE84qu9X8,5681
 dcnum/feat/gate.py,sha256=UEHbj3hkMWNm4tlY8Tz8sOsruhByjJxgO1s-ztQ7WTw,6235
-dcnum/feat/queue_event_extractor.py,sha256=_CwtEcJ-zzChkiPbRHC-WdVNy9sNWOYTzZPd2oEvtrU,11493
+dcnum/feat/queue_event_extractor.py,sha256=8IJZ6_2Snv0qr79hxKF-FPw9tBvTxbaLaZMYQyIZHyc,12375
 dcnum/feat/feat_background/__init__.py,sha256=mL8QJYK6m3hxTqF6Cuosu__Fm5tZUMa-hTgSGcNw9AE,458
 dcnum/feat/feat_background/base.py,sha256=YCkkxgl19dslqmbkbtMv8CH6oUrrdHmoheBlpDQZHa0,5021
 dcnum/feat/feat_background/bg_roll_median.py,sha256=3zwXlNE-CWu30RI8s3Z_ihKUPUVi_cm3yAaXIHlMz7Y,13626
@@ -31,32 +31,10 @@ dcnum/segm/segmenter_gpu.py,sha256=F-6H425eQc9B2-k5PURJziU5uQubdF96GTkoysD2JDM,1
 dcnum/segm/segmenter_manager_thread.py,sha256=xtuk7gnk7xhoRoV_J97rrv7IR3JgeRvVewCDT-chqpk,5172
 dcnum/write/__init__.py,sha256=Oy-ORTyzUUswsaJvd0C6LyXtOgAY0iTIRqFNU9d7M8Y,160
 dcnum/write/deque_writer_thread.py,sha256=UUn5OYxDvckvhLw3llLYu7y8MI7RfsOhdJhMonKKB3k,1625
-dcnum/write/queue_collector_thread.py,sha256=Iw83KAcZu13elorHUOfJT6cVQntAKBLm6OVgkldjtL0,11088
+dcnum/write/queue_collector_thread.py,sha256=mO4sSDB9gQW9ttugqAFFEcXlxz2E5QDjQcdZU_NT-BY,11404
 dcnum/write/writer.py,sha256=aUg_F1Ocs_wkV47lJJgkqGa8IRFhHH30NI7q0VxBNUA,3092
-docs/conf.py,sha256=VqB1WtClmmAVdfQ45SLa3aG7t6g2AcDG_BI6MO7j4wI,3022
-docs/index.rst,sha256=eWjHCDrw_VEC885Z3ON_wX5p2FRn_DI12WjSt0WcU5g,431
-docs/requirements.txt,sha256=KA1AT05zfznj2eE8ixs9cikcl_MtWplqbiXhp4h0YsI,87
-docs/extensions/github_changelog.py,sha256=SEJkjEvVtJ-42daYkNbcr9mHmmO6ZjDs6phvnySlNAE,2375
-tests/conftest.py,sha256=bYh2DmQRP2TbkmLBdeiKF-nSv5IX1oUNWcwT6w_bEUw,577
-tests/helper_methods.py,sha256=MsCppTICPqv4vq-DhUBIKFyOhvRO_oS2O0Fb3OYhNxs,1855
-tests/requirements.txt,sha256=Mfj5F30ZlweJpp9LC64TVta_lq6G5AINIfJxVxTK-2c,20
-tests/test_feat_background_bg_roll_median.py,sha256=FtrVcKumIctUrCWtNimGicExsouFxoZpbCwPnmeY1BU,4809
-tests/test_feat_brightness.py,sha256=V8F_zhxYvS0rrZl_SKZwVwpPLI6jq0J7NR-eOdNS6qg,2082
-tests/test_feat_haralick.py,sha256=_00p24WOzIOAtfKiXWcd8XoYBQKt3DbYdSijHZYzi64,3499
-tests/test_feat_moments_based.py,sha256=wRlqM8sGSPIzUB95gUuixNH1hTLgD7otj15-53CRxcE,3037
-tests/test_init.py,sha256=umUGuhCJ4iCsI5qjoNtrIAW_3xFfI3rDEGk8BKgzekc,73
-tests/test_ppid.py,sha256=gyrFLROG9IZIcHb0YQCHujTw-LdzGYTKZhJRAFgza6c,2785
-tests/test_ppid_segm.py,sha256=4NzGXns3lMetH970SKMnzizbnThx8ku4A1MiTozXMlA,238
-tests/test_read_concat_hdf5.py,sha256=jeOxG6T_Z8wtPVK_UbEa-X-VQtYdFCLE2oxFbWjN2iU,1951
-tests/test_read_hdf5.py,sha256=nEtjLI1oF5W0Ab_sJ0xLYctD8oR24OwORcj6sfG57Y4,6671
-tests/test_segm_thresh.py,sha256=ecHbhwy8_qVJTdpDJlo_sIiQPSIi_xKXM2EqUJXRU20,5101
-tests/test_segmenter.py,sha256=qjHTTUmaR08X4ATjndxJr9eZWFvpPQwJ_fSCw8-tr9Y,9307
-tests/test_write_deque_writer_thread.py,sha256=EAnqKayr4_jskv_599QYD3gdBZhtyVM7-MuqvtLHYAI,1140
-tests/test_write_writer.py,sha256=SzNTLsHz4RZceRwqflc4Wfn02vYc4Hb4WQVk1X8dmiw,1107
-tests/data/fmt-hdf5_cytoshot_full-features_2023.zip,sha256=LfkFxAXTIkcqxrJYYNMC364Q1x5HT5X9cTHuNz5eeuk,650653
-tests/data/fmt-hdf5_cytoshot_full-features_legacy_allev_2023.zip,sha256=z2Bk6u3wjr-bJa7sOxBcNKOQ0Zoi3Xmf_cMi6d-3CMk,154010
-dcnum-0.11.4.dist-info/LICENSE,sha256=YRChA1C8A2E-amJbudwMcbTCZy_HzmeY0hMIvduh1MM,1089
-dcnum-0.11.4.dist-info/METADATA,sha256=Hr8-6f7PT7eR9dUfCGG9xhVivAlpDSCNElVRMS9yWk8,2180
-dcnum-0.11.4.dist-info/WHEEL,sha256=AtBG6SXL3KF_v0NxLf0ehyVOh0cold-JbJYXNGorC6Q,92
-dcnum-0.11.4.dist-info/top_level.txt,sha256=Utc_P-_-7hbtniTp00IsHTry4h3rY5KFmwHfYM9g44k,22
-dcnum-0.11.4.dist-info/RECORD,,
+dcnum-0.11.6.dist-info/LICENSE,sha256=YRChA1C8A2E-amJbudwMcbTCZy_HzmeY0hMIvduh1MM,1089
+dcnum-0.11.6.dist-info/METADATA,sha256=5nNFMRnm1iAuuK_hX7m0alvm-P_ISS7FEGQrbNKI828,2180
+dcnum-0.11.6.dist-info/WHEEL,sha256=AtBG6SXL3KF_v0NxLf0ehyVOh0cold-JbJYXNGorC6Q,92
+dcnum-0.11.6.dist-info/top_level.txt,sha256=Hmh38rgG_MFTVDpUDGuO2HWTSq80P585Het4COQzFTg,6
+dcnum-0.11.6.dist-info/RECORD,,

dcnum-0.11.6.dist-info/top_level.txt

@@ -0,0 +1 @@
+dcnum

dcnum-0.11.4.dist-info/top_level.txt

@@ -1,4 +0,0 @@
-dcnum
-dist
-docs
-tests

docs/conf.py

@@ -1,87 +0,0 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-import pathlib
-import sys
-
-import dcnum
-
-sys.path.insert(0, str(pathlib.Path(__file__).parent / "extensions"))
-
-# -- Project information -----------------------------------------------------
-
-project = 'dcnum'
-copyright = '2023, Paul Müller'
-author = 'Paul Müller'
-
-
-# -- General configuration ---------------------------------------------------
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = ['sphinx.ext.autodoc',
-              'sphinx.ext.autosummary',
-              'sphinx.ext.intersphinx',
-              'sphinx.ext.mathjax',
-              'sphinx.ext.viewcode',
-              'sphinx.ext.napoleon',
-              'matplotlib.sphinxext.plot_directive',
-              'IPython.sphinxext.ipython_directive',
-              'IPython.sphinxext.ipython_console_highlighting',
-              'github_changelog',
-              ]
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
-
-
-# -- Options for HTML output -------------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = 'sphinx_rtd_theme'
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-#
-# The full version, including alpha/beta/rc tags.
-# This gets 'version'
-release = dcnum.__version__
-
-# enable enumeration of figures
-numfig = True
-
-# include source of matplotlib plots
-plot_include_source = True
-
-# http://www.sphinx-doc.org/en/stable/ext/autodoc.html#confval-autodoc_member_order
-# Order class attributes and functions in separate blocks
-autodoc_member_order = 'groupwise'
-autoclass_content = 'both'

docs/extensions/github_changelog.py

@@ -1,75 +0,0 @@
-"""Display changelog with links to GitHub issues
-
-Usage
------
-The directive
-
-   .. include_changelog:: ../CHANGELOG
-
-adds the content of the changelog file into the current document.
-References to GitHub issues are identified as "(#XY)" (with parentheses
-and hash) and a link is inserted
-
- https://github.com/RI-imaging/{PROJECT}/issues/{XY}
-
-where PROJECT ist the `project` variable defined in conf.py.
-"""
-import io
-import re
-
-from docutils.statemachine import ViewList
-from docutils.parsers.rst import Directive
-from sphinx.util.nodes import nested_parse_with_titles
-from docutils import nodes
-
-
-class IncludeDirective(Directive):
-    required_arguments = 1
-    optional_arguments = 0
-
-    def run(self):
-        full_path = self.arguments[0]
-        project = self.state.document.settings.env.config.github_project
-
-        def insert_github_link(reobj):
-            line = reobj.string
-            instr = line[reobj.start():reobj.end()]
-            issue = instr.strip("#()")
-            link = "https://github.com/{}/issues/".format(project)
-            rstlink = "(`#{issue} <{link}{issue}>`_)".format(issue=issue,
-                                                             link=link)
-            return rstlink
-
-        with io.open(full_path, "r") as myfile:
-            text = myfile.readlines()
-
-        rst = []
-        for line in text:
-            line = line.strip("\n")
-            if line.startswith("  ") and line.strip().startswith("-"):
-                # list in list:
-                rst.append("")
-            if not line.startswith(" "):
-                rst.append("")
-                line = "version " + line
-                rst.append(line)
-                rst.append("-"*len(line))
-            elif not line.strip():
-                rst.append(line)
-            else:
-                line = re.sub(r"\(#[0-9]*\)", insert_github_link, line)
-                rst.append(line)
-
-        vl = ViewList(rst, "fakefile.rst")
-        # Create a node.
-        node = nodes.section()
-        node.document = self.state.document
-        # Parse the rst.
-        nested_parse_with_titles(self.state, vl, node)
-        return node.children
-
-
-def setup(app):
-    app.add_config_value('github_project', "user/project", 'html')
-    app.add_directive('include_changelog', IncludeDirective)
-    return {'version': '0.1'}   # identifies the version of our extension

docs/index.rst

@@ -1,20 +0,0 @@
-.. dcnum documentation master file, created by
-   sphinx-quickstart on Fri Jun  2 23:46:40 2023.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to dcnum's documentation!
-=================================
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

docs/requirements.txt

@@ -1,7 +0,0 @@
-# requirement on rtd
-h5py
-ipython
-matplotlib
-numpy
-sphinx==4.2.0
-sphinx_rtd_theme==1.0

tests/conftest.py

@@ -1,20 +0,0 @@
-import atexit
-import os
-import shutil
-import tempfile
-import time
-
-TMPDIR = tempfile.mkdtemp(prefix=time.strftime(
-    "dcnum_test_%H.%M_"))
-
-
-def pytest_configure(config):
-    """
-    Allows plugins and conftest files to perform initial configuration.
-    This hook is called for every plugin and initial conftest
-    file after command line options have been parsed.
-    """
-    tempfile.tempdir = TMPDIR
-    atexit.register(shutil.rmtree, TMPDIR, ignore_errors=True)
-    # Disable JIT compiler during testing for coverage
-    os.environ.setdefault("NUMBA_DISABLE_JIT", "1")

tests/helper_methods.py

@@ -1,72 +0,0 @@
-import pathlib
-import tempfile
-import zipfile
-
-
-def calltracker(func):
-    """Decorator to track how many times a function is called"""
-
-    def wrapped(*args, **kwargs):
-        wrapped.calls += 1
-        return func(*args, **kwargs)
-
-    wrapped.calls = 0
-    return wrapped
-
-
-def find_data(path):
-    """Find .avi and .rtdc data files in a directory"""
-    path = pathlib.Path(path)
-    avifiles = [r for r in path.rglob("*.avi") if r.is_file()]
-    rtdcfiles = [r for r in path.rglob("*.rtdc") if r.is_file()]
-    files = [pathlib.Path(ff) for ff in rtdcfiles + avifiles]
-    return files
-
-
-def retrieve_data(zip_file):
-    """Extract contents of data zip file and return data files
-    """
-    zpath = pathlib.Path(__file__).resolve().parent / "data" / zip_file
-    # unpack
-    arc = zipfile.ZipFile(str(zpath))
-
-    # extract all files to a temporary directory
-    edest = tempfile.mkdtemp(prefix=zpath.name)
-    arc.extractall(edest)
-
-    # Load RT-DC dataset
-    # find tdms files
-    datafiles = find_data(edest)
-
-    if len(datafiles) == 1:
-        datafiles = datafiles[0]
-
-    return datafiles
-
-
-def find_model(path):
-    """Find .ckp files in a directory"""
-    path = pathlib.Path(path)
-    jit_files = [r for r in path.rglob("*.ckp") if r.is_file()]
-    files = [pathlib.Path(ff) for ff in jit_files]
-    return files
-
-
-def retrieve_model(zip_file):
-    """Extract contents of model zip file and return model ckeckpoint paths
-    """
-    zpath = pathlib.Path(__file__).resolve().parent / "data" / zip_file
-    # unpack
-    arc = zipfile.ZipFile(str(zpath))
-
-    # extract all files to a temporary directory
-    edest = tempfile.mkdtemp(prefix=zpath.name)
-    arc.extractall(edest)
-
-    # find model checkpoint paths
-    modelpaths = find_model(edest)
-
-    if len(modelpaths) == 1:
-        modelpaths = modelpaths[0]
-
-    return modelpaths

tests/requirements.txt

@@ -1,2 +0,0 @@
-pytest
-scikit-image

tests/test_feat_background_bg_roll_median.py

@@ -1,131 +0,0 @@
-import h5py
-import numpy as np
-import pytest
-
-from dcnum.feat.feat_background import bg_roll_median
-
-
-def test_compute_median_for_slice():
-    # events in shared arrays: 100
-    # image shape: 5 * 7
-    shared_input = np.arange(5*7).reshape(1, 5*7) * np.ones((100, 1))
-    assert shared_input.size == 100 * 5 * 7
-    assert np.all(shared_input[:, 0] == 0)  # pixel 0
-    assert np.all(shared_input[:, 1] == 1)  # pixel 1
-
-    shared_output = np.zeros((100, 5 * 7))
-
-    job_slice = slice(1, 4)
-
-    batch_size = 90
-    kernel_size = 10
-
-    bg_roll_median.compute_median_for_slice(
-        shared_input=shared_input,
-        shared_output=shared_output,
-        job_slice=job_slice,
-        output_size=batch_size,
-        kernel_size=kernel_size,
-    )
-
-    # compare input and output at batch size
-    assert np.all(shared_input[:90, 1:4] == shared_input[:90, 1:4])
-
-    # sanity check with boundary values
-    comp_in_b = shared_input.reshape(-1, 100)[1:4, 90:]
-    comp_out_b = shared_output.reshape(-1, 100)[1:4, 90:]
-    assert not np.all(comp_in_b == comp_out_b)
-
-
-@pytest.mark.parametrize("event_count", [720, 730])  # should be independent
-def test_median_map_iterator(tmp_path, event_count):
-    output_path = tmp_path / "test.h5"
-    # batch size: 90
-    # image shape: 5 * 7
-    # kernel size: 10
-    input_data = np.arange(5*7).reshape(1, 5, 7) * np.ones((event_count, 1, 1))
-    assert np.all(input_data[0] == input_data[1])
-    assert np.all(input_data[0].flatten() == np.arange(5*7))
-
-    with bg_roll_median.BackgroundRollMed(input_data=input_data,
-                                          output_path=output_path,
-                                          kernel_size=10,
-                                          batch_size=90,
-                                          ) as mic:
-        assert len(mic.shared_input_raw) == (10 + 90) * 5 * 7
-
-        jobs = list(mic.map_iterator())
-    assert len(jobs) == 7
-    assert jobs[1].start == 1 * 5
-    assert jobs[1].stop == 2 * 5
-    assert jobs[2].start == 2 * 5
-    assert jobs[2].stop == 3 * 5
-    assert jobs[6].stop == 7 * 5
-
-
-@pytest.mark.parametrize("event_count", [720, 730])
-def test_median_process_next_batch(tmp_path, event_count):
-    output_path = tmp_path / "test.h5"
-    # batch size: 90
-    # image shape: 5 * 7
-    # kernel size: 10
-    input_data = np.arange(5*7).reshape(1, 5, 7) * np.ones((event_count, 1, 1))
-    input_data = np.array(input_data, dtype=np.uint8)
-    assert np.all(input_data[0] == input_data[1])
-    assert np.all(input_data[0].flatten() == np.arange(5*7))
-
-    with bg_roll_median.BackgroundRollMed(input_data=input_data,
-                                          output_path=output_path,
-                                          kernel_size=10,
-                                          batch_size=90,
-                                          ) as mic:
-        assert len(mic.shared_input_raw) == (10 + 90) * 5 * 7
-
-        assert mic.current_batch == 0
-        mic.process_next_batch()
-
-        assert mic.current_batch == 1
-
-    with h5py.File(output_path) as h5:
-        ds = h5["events/image_bg"]
-        assert ds.shape == (event_count, 5, 7)
-        assert np.all(ds[90:] == 0), "not processed"
-        assert np.all(ds[:90, 0, 0] == 0)
-        assert np.all(ds[:90, 0, 1] == 1)
-        assert np.all(ds[:90, 0, 2] == 2)
-        assert np.all(ds[:90, 1, 0] == 7)
-
-
-@pytest.mark.parametrize("event_count, chunk_count", [[720, 8], [730, 9]])
-def test_median_process_full(tmp_path, event_count, chunk_count):
-    output_path = tmp_path / "test.h5"
-    # batch size: 90
-    # image shape: 5 * 7
-    # kernel size: 10
-    input_data = np.arange(5*7).reshape(1, 5, 7) * np.ones((event_count, 1, 1))
-    input_data = np.array(input_data, dtype=np.uint8)
-    assert np.all(input_data[0] == input_data[1])
-    assert np.all(input_data[0].flatten() == np.arange(5*7))
-
-    with bg_roll_median.BackgroundRollMed(input_data=input_data,
-                                          output_path=output_path,
-                                          kernel_size=10,
-                                          batch_size=90,
-                                          ) as mic:
-        assert len(mic.shared_input_raw) == (10 + 90) * 5 * 7
-        # output array is smaller
-        assert len(mic.shared_output_raw) == 90 * 5 * 7
-
-        assert mic.current_batch == 0
-        mic.process()
-        assert mic.current_batch == chunk_count
-
-    with h5py.File(output_path) as h5:
-        ds = h5["events/image_bg"]
-        assert ds.shape == (event_count, 5, 7)
-        assert np.all(ds[:90, 0, 0] == 0)
-        assert np.all(ds[:90, 0, 1] == 1)
-        assert np.all(ds[:90, 0, 2] == 2)
-        assert np.all(ds[:90, 1, 0] == 7)
-        assert np.all(ds[690:, 0, 0] == 0)
-        assert np.all(ds[690:, 0, 1] == 1)

tests/test_feat_brightness.py

@@ -1,56 +0,0 @@
-import pathlib
-
-import h5py
-import numpy as np
-
-from dcnum.feat import feat_brightness
-
-from helper_methods import retrieve_data
-
-data_path = pathlib.Path(__file__).parent / "data"
-
-
-def test_basic_brightness():
-    # This original file was generated with dcevent for reference.
-    path = retrieve_data(data_path /
-                         "fmt-hdf5_cytoshot_full-features_2023.zip")
-    # Make data available
-    with h5py.File(path) as h5:
-        data = feat_brightness.brightness_features(
-            image=h5["events/image"][:],
-            image_bg=h5["events/image_bg"][:],
-            mask=h5["events/mask"][:],
-        )
-
-        assert np.allclose(data["bright_bc_avg"][1],
-                           -43.75497215592681,
-                           atol=0, rtol=1e-10)
-        for feat in feat_brightness.brightness_names:
-            assert np.allclose(h5["events"][feat][:],
-                               data[feat]), f"Feature {feat} mismatch!"
-        # control test
-        assert not np.allclose(h5["events"]["bright_perc_10"][:],
-                               data["bright_perc_90"])
-
-
-def test_basic_brightness_single_image():
-    # This original file was generated with dcevent for reference.
-    path = retrieve_data(data_path /
-                         "fmt-hdf5_cytoshot_full-features_2023.zip")
-    # Make data available
-    with h5py.File(path) as h5:
-        data = feat_brightness.brightness_features(
-            image=h5["events/image"][1][np.newaxis],
-            image_bg=h5["events/image_bg"][1][np.newaxis],
-            mask=h5["events/mask"][1][np.newaxis],
-        )
-
-        assert np.allclose(data["bright_bc_avg"][0],
-                           -43.75497215592681,
-                           atol=0, rtol=1e-10)
-        for feat in feat_brightness.brightness_names:
-            assert np.allclose(h5["events"][feat][1],
-                               data[feat][0]), f"Feature {feat} mismatch!"
-        # control test
-        assert not np.allclose(h5["events"]["bright_perc_10"][1],
-                               data["bright_perc_90"][0])