dcnum 0.24.0__py3-none-any.whl → 0.25.0__py3-none-any.whl

dcnum/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.24.0'
-__version_tuple__ = version_tuple = (0, 24, 0)
+__version__ = version = '0.25.0'
+__version_tuple__ = version_tuple = (0, 25, 0)

dcnum/feat/feat_background/bg_sparse_median.py

@@ -59,7 +59,7 @@ class BackgroundSparseMed(Background):
         offset_correction: bool
             The sparse median background correction produces one median
             image for multiple input frames (BTW this also leads to very
-            efficient data storage with HDF5 data compression filters). In
+            efficient data storage with internal HDF5 basins). In
             case the input frames are subject to frame-by-frame brightness
             variations (e.g. flickering of the illumination source), it
             is useful to have an offset value per frame that can then be
@@ -226,7 +226,7 @@ class BackgroundSparseMed(Background):
         offset_correction: bool
             The sparse median background correction produces one median
             image for multiple input frames (BTW this also leads to very
-            efficient data storage with HDF5 data compression filters). In
+            efficient data storage with internal HDF5 basins). In
             case the input frames are subject to frame-by-frame brightness
             variations (e.g. flickering of the illumination source), it
             is useful to have an offset value per frame that can then be

dcnum/meta/ppid.py

@@ -7,6 +7,7 @@ import pathlib
 from typing import Dict, List, Protocol
 import warnings
 
+import numpy as np
 
 #: Increment this string if there are breaking changes that make
 #: previous pipelines unreproducible.
@@ -140,9 +141,9 @@ def kwargs_to_ppid(cls: ClassWithPPIDCapabilities,
                 path = pathlib.Path(val)
                 if path.exists():
                     val = path.name
-            if isinstance(val, bool):
+            if isinstance(val, (bool, np.bool_)):
                 val = int(val)  # do not print e.g. "True"
-            elif isinstance(val, float):
+            elif isinstance(val, (float, np.floating)):
                 if val == int(val):
                     val = int(val)  # omit the ".0" at the end
             concat_strings.append(f"{abr}={val}")

dcnum/read/__init__.py

@@ -1,5 +1,6 @@
 # flake8: noqa: F401
 from .cache import md5sum
 from .const import PROTECTED_FEATURES
+from .detect_flicker import detect_flickering
 from .hdf5_data import HDF5Data, HDF5ImageCache, concatenated_hdf5_data
 from .mapped import get_mapping_indices, get_mapped_object

dcnum/read/cache.py

@@ -36,9 +36,10 @@ class BaseImageChunkCache(abc.ABC):
     def __getitem__(self, index):
         if isinstance(index, (slice, list, np.ndarray)):
             if isinstance(index, slice):
-                indices = np.arange(index.start or 0,
-                                    index.stop or len(self),
-                                    index.step)
+                indices = np.arange(
+                    index.start or 0,
+                    min(index.stop, len(self)) if index.stop else len(self),
+                    index.step)
             else:
                 indices = index
             array_out = np.empty((len(indices),) + self.image_shape,

dcnum/read/detect_flicker.py

@@ -0,0 +1,44 @@
+import numpy as np
+
+from .hdf5_data import HDF5Data
+
+
+def detect_flickering(image_data: np.ndarray | HDF5Data,
+                      roi_height: int = 10,
+                      brightness_threshold: float = 2.5,
+                      count_threshold: int = 5,
+                      max_frames: int = 1000):
+    """Determine whether an image series experiences flickering
+
+    Flickering is an unwelcome phenomenon due to a faulty data
+    acquisition device. For instance, if there is random voltage noise in
+    the electronics managing the LED power, then the brightness of the
+    LED will vary randomly when the noise signal overlaps with the flash
+    triggering signal.
+
+    If flickering is detected, you should use the "sparsemed" background
+    computation with `offset_correction` set to True.
+
+    Parameters
+    ----------
+    image_data:
+        sliceable object (e.g. numpy array or HDF5Data) containing
+        image data.
+    roi_height: int
+        height of the ROI in pixels for which to search for flickering;
+        the entire width of the image is used
+    brightness_threshold: float
+        brightness difference between individual ROIs median and median
+        of all ROI medians leading to a positive flickering event
+    count_threshold: int
+        minimum number of flickering events that would lead to a positive
+        flickering decision
+    max_frames: int
+        maximum number of frames to include in the flickering analysis
+    """
+    # slice event axis first in case we have and HDF5Data instance
+    roi_data = image_data[:max_frames][:, :roi_height, :]
+    roi_median = np.median(roi_data, axis=(1, 2))
+    roi_offset = roi_median - np.median(roi_median)
+    flickering_events = np.sum(np.abs(roi_offset) >= abs(brightness_threshold))
+    return flickering_events >= count_threshold

{dcnum-0.24.0.dist-info → dcnum-0.25.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.24.0
+Version: 0.25.0
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller, Raghava Alajangi
 Maintainer-email: Paul Müller <dev@craban.de>

{dcnum-0.24.0.dist-info → dcnum-0.25.0.dist-info}/RECORD

@@ -1,5 +1,5 @@
 dcnum/__init__.py,sha256=hcawIKS7utYiOyVhOAX9t7K3xYzP1b9862VV0b6qSrQ,74
-dcnum/_version.py,sha256=DKJfCmnOSzDR_ntzwRoytwuILw8hpyVnYbxMRkBXRw4,413
+dcnum/_version.py,sha256=nhq2LDshqyJE9A3DLIz_6mBkgGLKSQrYmHfzZ_jVCbc,413
 dcnum/feat/__init__.py,sha256=jUJYWTD3VIoDNKrmryXbjHb1rGwYtK4b7VPWihYgUoo,325
 dcnum/feat/event_extractor_manager_thread.py,sha256=FAxSyRfaNAuBWNplxHngp5h-44s0qIP24XX_oETdfMk,7836
 dcnum/feat/gate.py,sha256=Yhxq80JoRMmQzBxl35C8NT91c9QcmQa-EIKLuxK6WvE,7221
@@ -8,7 +8,7 @@ dcnum/feat/feat_background/__init__.py,sha256=OTmMuazHNaSrZb2XW4cnJ6PlgJLbKrPbai
 dcnum/feat/feat_background/base.py,sha256=bQBPvztrku-8YSVk8YBUUNh7MaYcnztgyD2-dQHxpzw,8674
 dcnum/feat/feat_background/bg_copy.py,sha256=PK8x4_Uph-_A6uszZC5uhe1gD1dSRdHnDMEsN0HSGHA,1034
 dcnum/feat/feat_background/bg_roll_median.py,sha256=EyjstMDXFBYuJB1lN6g4Uw7tPm434X3hXQxKSqvcoJ4,13175
-dcnum/feat/feat_background/bg_sparse_median.py,sha256=87tfB6MoNeTmv9vPBAbfkzNW1m7ESQOg_-rGvm8kY_k,22071
+dcnum/feat/feat_background/bg_sparse_median.py,sha256=wt7lvPSiZkdaerRErgezd_YDVxHA2kAqO1LMX9PuHJk,22053
 dcnum/feat/feat_brightness/__init__.py,sha256=o6AebVlmydwNgVF5kW6ITqJyFreoKrU3Ki_3EC8If-s,155
 dcnum/feat/feat_brightness/bright_all.py,sha256=vf8xaYBdKD24hHUXdkI0_S7nbr7m49KW6gvuWvbHDVg,4545
 dcnum/feat/feat_brightness/common.py,sha256=JX49EszYDmnvoOKXFVV1CalEIWRmOuY5EryNbqGbdac,156
@@ -25,10 +25,11 @@ dcnum/logic/job.py,sha256=9BN2WjYqjjJuLnfNZAtQ2Nn47Glo2jVrivDodGJoqlQ,7713
 dcnum/logic/json_encoder.py,sha256=cxMnqisbKEVf-rVcw6rK2BBAb6iz_hKFaGl81kK36lQ,571
 dcnum/meta/__init__.py,sha256=AVqRgyKXO1orKnE305h88IBvoZ1oz6X11HN1WP5nGvg,60
 dcnum/meta/paths.py,sha256=J_ikeHzd7gEeRgAKjuayz3x6q4h1fOiDadM-ZxhAGm4,1053
-dcnum/meta/ppid.py,sha256=X46w3hoBW0zxKY1avokC2Wex6E3aqV4LaMmpbCFYrXg,8432
-dcnum/read/__init__.py,sha256=ksLdV8EkOU3EPje8teCOSehcUeGAZfg9TQ5ltuEUgls,216
-dcnum/read/cache.py,sha256=lisrGG7AyvVitf0h92wh5FvYCsxa0pWyGcAyYwGP-LQ,6471
+dcnum/meta/ppid.py,sha256=RnDkJSdV1kDznAsOhQN5WI7uC9UwSMCjyADP7yWNvkM,8478
+dcnum/read/__init__.py,sha256=LYHyZHgiNTpjV5oEcty-7Kh5topLpHT_cFlNl-QX8gg,262
+dcnum/read/cache.py,sha256=LNA5nnDyrw8Nj07E7XfG2GcHEoWm6vA6Qo_8N-n-sGw,6492
 dcnum/read/const.py,sha256=GG9iyXDtEldvJYOBnhZjlimzIeBMAt4bSr2-xn2gzzc,464
+dcnum/read/detect_flicker.py,sha256=CeUyxI6LaX_lCNvBPm_yzsiWmiNcZYqbNZCtvKPdkcU,1827
 dcnum/read/hdf5_data.py,sha256=JVk9YWw1rPgTPxaMZsw2ehk4FJq9UqhmB1SW7yhPw50,25867
 dcnum/read/mapped.py,sha256=zU2fYdZfLNHn0rKHxDzBhNFMu4--WWa8nSeE2likyZA,3637
 dcnum/segm/__init__.py,sha256=9cLEAd3JWE8IGqDHV-eSDIYOGBfOepd8OcebtNs8Omk,309
@@ -48,8 +49,8 @@ dcnum/write/__init__.py,sha256=sK79IlvCFIqf2oFABVeyYedMnHOsEIQpxAauEeNO-Tw,273
 dcnum/write/deque_writer_thread.py,sha256=ao7F1yrVKyufgC4rC0Y2_Vt7snuT6KpI7W2qVxcjdhk,1994
 dcnum/write/queue_collector_thread.py,sha256=d_WfdsZdFnFsiAY0zVMwUlA4juIMeiWYmE_-rezBQCE,11734
 dcnum/write/writer.py,sha256=sFt4O9O4uUabxmBZu776b5pBf_DPDpsz-jLpSsswQ1g,20531
-dcnum-0.24.0.dist-info/LICENSE,sha256=YRChA1C8A2E-amJbudwMcbTCZy_HzmeY0hMIvduh1MM,1089
-dcnum-0.24.0.dist-info/METADATA,sha256=gvvl8eJLQNtI-p6FUE-AZs1sZ8ZnBwgpT1vVmczgxEs,2280
-dcnum-0.24.0.dist-info/WHEEL,sha256=mguMlWGMX-VHnMpKOjjQidIo1ssRlCFu4a4mBpz1s2M,91
-dcnum-0.24.0.dist-info/top_level.txt,sha256=Hmh38rgG_MFTVDpUDGuO2HWTSq80P585Het4COQzFTg,6
-dcnum-0.24.0.dist-info/RECORD,,
+dcnum-0.25.0.dist-info/LICENSE,sha256=YRChA1C8A2E-amJbudwMcbTCZy_HzmeY0hMIvduh1MM,1089
+dcnum-0.25.0.dist-info/METADATA,sha256=CNZS4i26iGkFnwde0p0I8xzD80cRqKrDRQssMXnqkSo,2280
+dcnum-0.25.0.dist-info/WHEEL,sha256=Wyh-_nZ0DJYolHNn1_hMa4lM7uDedD_RGVwbmTjyItk,91
+dcnum-0.25.0.dist-info/top_level.txt,sha256=Hmh38rgG_MFTVDpUDGuO2HWTSq80P585Het4COQzFTg,6
+dcnum-0.25.0.dist-info/RECORD,,

{dcnum-0.24.0.dist-info → dcnum-0.25.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.1.1)
+Generator: setuptools (71.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any