dcnum 0.25.8__py3-none-any.whl → 0.25.10__py3-none-any.whl

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Files changed (8) hide show
  1. dcnum/_version.py +2 -2
  2. dcnum/feat/feat_background/base.py +5 -2
  3. dcnum/segm/segm_torch/segm_torch_base.py +11 -4
  4. {dcnum-0.25.8.dist-info → dcnum-0.25.10.dist-info}/METADATA +1 -1
  5. {dcnum-0.25.8.dist-info → dcnum-0.25.10.dist-info}/RECORD +8 -8
  6. {dcnum-0.25.8.dist-info → dcnum-0.25.10.dist-info}/WHEEL +1 -1
  7. {dcnum-0.25.8.dist-info → dcnum-0.25.10.dist-info}/licenses/LICENSE +0 -0
  8. {dcnum-0.25.8.dist-info → dcnum-0.25.10.dist-info}/top_level.txt +0 -0
dcnum/_version.py CHANGED
@@ -17,5 +17,5 @@ __version__: str
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  __version_tuple__: VERSION_TUPLE
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  version_tuple: VERSION_TUPLE
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- __version__ = version = '0.25.8'
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- __version_tuple__ = version_tuple = (0, 25, 8)
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+ __version__ = version = '0.25.10'
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+ __version_tuple__ = version_tuple = (0, 25, 10)
dcnum/feat/feat_background/base.py CHANGED
@@ -9,7 +9,7 @@ import time
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  import h5py
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  from ...meta import ppid
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- from ...read import HDF5Data
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+ from ...read import HDF5Data, md5sum
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  from ...write import HDF5Writer, create_with_basins, set_default_filter_kwargs
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@@ -87,6 +87,9 @@ class Background(abc.ABC):
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  # Check whether user passed an array or a path
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  if isinstance(input_data, pathlib.Path):
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+ # Compute MD5 sum before opening the file so that we don't
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+ # get a file-locking issue (PermissionError) on Windows.
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+ md5_5m = md5sum(input_data, blocksize=65536, count=80)
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  if str(input_data.resolve()) == str(output_path.resolve()):
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  self.h5in = h5py.File(input_data, "a", libver="latest")
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  self.h5out = self.h5in
@@ -98,7 +101,7 @@ class Background(abc.ABC):
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  # the ImageCache. We have to go via the ImageCache route,
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  # because HDF5Data properly resolves basins and the image
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  # feature might be in a basin.
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- self.hdin = HDF5Data(self.h5in)
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+ self.hdin = HDF5Data(self.h5in, md5_5m=md5_5m)
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  self.input_data = self.hdin.image.h5ds
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  else:
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  self.input_data = input_data
dcnum/segm/segm_torch/segm_torch_base.py CHANGED
@@ -3,6 +3,8 @@ import pathlib
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  import re
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  from typing import Dict
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+ import numpy as np
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+
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  from ...meta import paths
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  from ..segmenter import Segmenter, SegmenterNotApplicableError
@@ -116,10 +118,15 @@ class TorchSegmenterBase(Segmenter):
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  """
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  key = item["key"]
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  if key in data_dict:
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- regexp = re.compile(item["regexp"])
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- matched = bool(regexp.match(data_dict[key]))
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- negate = item.get("regexp-negate", False)
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- valid = matched if not negate else not matched
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+ valid = True
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+ if "regexp" in item:
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+ re_match = bool(re.search(item["regexp"], data_dict[key],
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+ re.MULTILINE))
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+ negate = item.get("regexp-negate", False)
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+ valid = valid and (re_match if not negate else not re_match)
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+ if "value" in item:
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+ valid = valid and np.allclose(item["value"], data_dict[key],
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+ atol=0, rtol=0.01)
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  if not valid:
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  reasons_list.append(item.get("reason", "unknown reason"))
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  elif not item.get("allow-missing-key", False):
{dcnum-0.25.8.dist-info → dcnum-0.25.10.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: dcnum
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- Version: 0.25.8
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+ Version: 0.25.10
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  Summary: numerics toolbox for imaging deformability cytometry
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  Author: Maximilian Schlögel, Paul Müller, Raghava Alajangi
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  Maintainer-email: Paul Müller <dev@craban.de>
{dcnum-0.25.8.dist-info → dcnum-0.25.10.dist-info}/RECORD RENAMED
@@ -1,12 +1,12 @@
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  dcnum/__init__.py,sha256=p0mYg01FQ6nsERYmx_FfVxqqHvYcSMEyIAMBIivAmO8,1206
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- dcnum/_version.py,sha256=IPFZ9tPIaduJC_jCnw8B-tCFsabLErCwnlpnrnKHV6M,513
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+ dcnum/_version.py,sha256=2u4bWaMdcZXyf4_yxgykEAXNXcEaVQumowHKcuxLJUI,515
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  dcnum/os_env_st.py,sha256=4psq-gPuWTTQ118kCiTx0Mhoyads4Irn6JSUzZk8gyc,3052
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  dcnum/feat/__init__.py,sha256=jUJYWTD3VIoDNKrmryXbjHb1rGwYtK4b7VPWihYgUoo,325
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  dcnum/feat/event_extractor_manager_thread.py,sha256=6D3RVYBuH7gOoGZ4Kz74n6fhq7MtlTY26kpSwZRqg3M,7972
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  dcnum/feat/gate.py,sha256=EOleB83sOlBjc8bjaZfWwGuxfCcEO5mknuFunlw_j7o,7252
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  dcnum/feat/queue_event_extractor.py,sha256=s-sC7Inkly_HYbqT3OPB6zWRvKm4TNOewujt1EuZF4M,16183
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  dcnum/feat/feat_background/__init__.py,sha256=OTmMuazHNaSrZb2XW4cnJ6PlgJLbKrPbaidpEixYa0A,341
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- dcnum/feat/feat_background/base.py,sha256=N2_CqA1LJwvsfhr3xMPbicVs3DVDXtvlNDZ-uPrJi5w,8749
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+ dcnum/feat/feat_background/base.py,sha256=pWxMCBg2NbO6uGMPl3b-Ia1eXlfHNFsNG5JjWqAFZKI,8979
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  dcnum/feat/feat_background/bg_copy.py,sha256=Xfju4DqbrtPyaUf3x-ybrWci5ip_cEbeiEg7Jh56YIY,1182
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  dcnum/feat/feat_background/bg_roll_median.py,sha256=rb3JnFzm4aXVLMKdP9wJlRXwTwmKUz2R1RBS9GXPepg,13622
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  dcnum/feat/feat_background/bg_sparse_median.py,sha256=PbcTehk46b9l03ZA1mBdyeMPHmGgGN4-59eLy2TzwX8,22634
@@ -41,7 +41,7 @@ dcnum/segm/segmenter_manager_thread.py,sha256=vMZFBa18oO8OyVB3niy_mtEfKkGOWHEga4
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  dcnum/segm/segmenter_mpo.py,sha256=O6G4xzHKNMSmyX9HDXTfl-3f9Fk2filxvVrRIO2D9hg,14117
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  dcnum/segm/segmenter_sto.py,sha256=C55orEAZtMowNwtAT_WdSv46n5CzgLFuGq9kwdHc97I,3963
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  dcnum/segm/segm_torch/__init__.py,sha256=DtUqJTbj7ybrTbXlwHq1Y4SCzi22rMW9Cus6wX-iU-A,822
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- dcnum/segm/segm_torch/segm_torch_base.py,sha256=Z2c9_lZI4qEljQEMXuN_6CpBti57PbbjlDq0NGX3-EU,4514
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+ dcnum/segm/segm_torch/segm_torch_base.py,sha256=wPt5QAmBDQxAA3Zxrdj3l9di0nIQmlUmKVJWtEpahH8,4814
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  dcnum/segm/segm_torch/segm_torch_mpo.py,sha256=GOva6o-6_SppxWD4BeBB3ap1TR-6rIYHavtfIstaYvc,2643
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  dcnum/segm/segm_torch/segm_torch_sto.py,sha256=PTOJrP_FkaxZZul8lM4VA2HL3KyxrheDDWWdJbmJdiw,3393
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  dcnum/segm/segm_torch/torch_model.py,sha256=5aL6SwSvg1N2gATEGBhP3aA4WTHlvGzQVYuizmh0LrU,3187
@@ -51,8 +51,8 @@ dcnum/write/__init__.py,sha256=sK79IlvCFIqf2oFABVeyYedMnHOsEIQpxAauEeNO-Tw,273
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  dcnum/write/deque_writer_thread.py,sha256=ao7F1yrVKyufgC4rC0Y2_Vt7snuT6KpI7W2qVxcjdhk,1994
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  dcnum/write/queue_collector_thread.py,sha256=-p5vrk9cDhtaIMFIu_cCmvlZJafrFkW68uONonMURYo,11617
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  dcnum/write/writer.py,sha256=JkVb4KDBV3oo9r3p2yy9wECO1REx7FG0PRBmVWTxJdk,20577
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- dcnum-0.25.8.dist-info/licenses/LICENSE,sha256=rX7tNSxP-EhLz-yYUyoBGwjJheA2fiZpT1Iw0LXnJ2M,1069
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- dcnum-0.25.8.dist-info/METADATA,sha256=MH79v2fgGvYk_cmCvPoJij9jVq1LUY-7VHT62Y986PY,2354
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- dcnum-0.25.8.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
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- dcnum-0.25.8.dist-info/top_level.txt,sha256=Hmh38rgG_MFTVDpUDGuO2HWTSq80P585Het4COQzFTg,6
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- dcnum-0.25.8.dist-info/RECORD,,
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+ dcnum-0.25.10.dist-info/licenses/LICENSE,sha256=rX7tNSxP-EhLz-yYUyoBGwjJheA2fiZpT1Iw0LXnJ2M,1069
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+ dcnum-0.25.10.dist-info/METADATA,sha256=twT_YXAb4Xxt24EKrjxEg8-4UgkHDHYOfzS-prFCXTM,2355
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+ dcnum-0.25.10.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ dcnum-0.25.10.dist-info/top_level.txt,sha256=Hmh38rgG_MFTVDpUDGuO2HWTSq80P585Het4COQzFTg,6
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+ dcnum-0.25.10.dist-info/RECORD,,
{dcnum-0.25.8.dist-info → dcnum-0.25.10.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
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  Wheel-Version: 1.0
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- Generator: setuptools (78.1.0)
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+ Generator: setuptools (80.9.0)
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  Root-Is-Purelib: true
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  Tag: py3-none-any
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