dcnum 0.25.0__py3-none-any.whl → 0.25.2__py3-none-any.whl

dcnum/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.25.0'
-__version_tuple__ = version_tuple = (0, 25, 0)
+__version__ = version = '0.25.2'
+__version_tuple__ = version_tuple = (0, 25, 2)

dcnum/logic/ctrl.py

@@ -679,8 +679,14 @@ class DCNumJobRunner(threading.Thread):
                     self.logger.debug(f"Creating basin for {feats}")
                     # Relative and absolute paths.
                     pin = pathlib.Path(hin.filename).resolve()
+                    paths = [pin]
                     pout = pathlib.Path(hout.filename).resolve().parent
-                    paths = [pin, os.path.relpath(pin, pout)]
+                    try:
+                        paths.append(os.path.relpath(pin, pout))
+                    except ValueError:
+                        # This means it is impossible to compute a relative
+                        # path (e.g. different drive letter on Windows).
+                        pass
                     hw.store_basin(name="dcnum basin",
                                    features=feats,
                                    mapping=basinmap0,
@@ -776,7 +782,6 @@ class DCNumJobRunner(threading.Thread):
 
         # Start the data collection thread
         thr_coll = QueueCollectorThread(
-            data=self.dtin,
             event_queue=fe_kwargs["event_queue"],
             writer_dq=writer_dq,
             feat_nevents=fe_kwargs["feat_nevents"],

dcnum/write/queue_collector_thread.py

@@ -8,8 +8,6 @@ from typing import List
 
 import numpy as np
 
-from ..read import HDF5Data
-
 
 class EventStash:
     def __init__(self,
@@ -61,11 +59,10 @@ class EventStash:
             Event dictionary
         """
         idx_loc = index - self.index_offset
-        idx_stop = self.nev_idx[idx_loc]
-        self._tracker[idx_loc] = True
 
         if events:
             slice_loc = None
+            idx_stop = self.nev_idx[idx_loc]
             for feat in events:
                 dev = events[feat]
                 if dev.size:
@@ -76,6 +73,8 @@ class EventStash:
             if slice_loc:
                 self.indices_for_data[slice_loc] = index
 
+        self._tracker[idx_loc] = True
+
     def require_feature(self, feat, sample_data):
         """Create a new empty feature array in `self.events` and return it
 
@@ -87,10 +86,10 @@ class EventStash:
             Sample data for one event of the feature (used to determine
             shape and dtype of the feature array)
         """
-        sample_data = np.array(sample_data)
-        event_shape = sample_data.shape
-        dtype = sample_data.dtype
         if feat not in self.events:
+            sample_data = np.array(sample_data)
+            event_shape = sample_data.shape
+            dtype = sample_data.dtype
             darr = np.zeros((self.size,) + tuple(event_shape),
                             dtype=dtype)
             self.events[feat] = darr
@@ -99,7 +98,6 @@ class EventStash:
 
 class QueueCollectorThread(threading.Thread):
     def __init__(self,
-                 data: HDF5Data,
                  event_queue: mp.Queue,
                  writer_dq: deque,
                  feat_nevents: mp.Array,
@@ -115,9 +113,6 @@ class QueueCollectorThread(threading.Thread):
 
         Parameters
         ----------
-        data:
-            Data source object. This is used for appending additional
-            information
         event_queue:
             A queue object to which other processes or threads write
             events as tuples `(frame_index, events_dict)`.
@@ -146,8 +141,6 @@ class QueueCollectorThread(threading.Thread):
         super(QueueCollectorThread, self).__init__(
               name="QueueCollector", *args, **kwargs)
         self.logger = logging.getLogger("dcnum.write.QueueCollector")
-        #: HDF5 data instance
-        self.data = data
         #: Event queue from which to collect event data
         self.event_queue = event_queue
         #: Writer deque to which event arrays are appended
@@ -169,7 +162,7 @@ class QueueCollectorThread(threading.Thread):
         # We are not writing to `event_queue` so we can safely cancel
         # our queue thread if we are told to stop.
         self.event_queue.cancel_join_thread()
-        # Indexes the current frame in `self.data`.
+        # Indexes the current frame in the input HDF5Data instance.
         last_idx = 0
         self.logger.debug("Started collector thread")
         while True:

dcnum/write/writer.py

@@ -140,10 +140,10 @@ class HDF5Writer:
                                                feat_dtype=feat_dtype),
                 **ds_kwds)
             if len(item_shape) == 2:
-                dset.attrs.create('CLASS', np.string_('IMAGE'))
-                dset.attrs.create('IMAGE_VERSION', np.string_('1.2'))
+                dset.attrs.create('CLASS', np.bytes_('IMAGE'))
+                dset.attrs.create('IMAGE_VERSION', np.bytes_('1.2'))
                 dset.attrs.create('IMAGE_SUBCLASS',
-                                  np.string_('IMAGE_GRAYSCALE'))
+                                  np.bytes_('IMAGE_GRAYSCALE'))
             offset = 0
         else:
             dset = egroup[feat]

{dcnum-0.25.0.dist-info → dcnum-0.25.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcnum
-Version: 0.25.0
+Version: 0.25.2
 Summary: numerics toolbox for imaging deformability cytometry
 Author: Maximilian Schlögel, Paul Müller, Raghava Alajangi
 Maintainer-email: Paul Müller <dev@craban.de>
@@ -17,14 +17,14 @@ Classifier: Intended Audience :: Science/Research
 Requires-Python: <4,>=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: h5py >=3.0.0
-Requires-Dist: hdf5plugin >=3.3.1
-Requires-Dist: mahotas
-Requires-Dist: numba
-Requires-Dist: numpy >=1.21
-Requires-Dist: opencv-python-headless
-Requires-Dist: scikit-image
-Requires-Dist: scipy >=1.8.0
+Requires-Dist: h5py <4,>=3.0.0
+Requires-Dist: hdf5plugin <6,>=3.3.1
+Requires-Dist: mahotas <2,>=1
+Requires-Dist: numba <1,>=0.60
+Requires-Dist: numpy <3,>=1.21
+Requires-Dist: opencv-python-headless <5,>=4
+Requires-Dist: scikit-image <1,>=0.24
+Requires-Dist: scipy <2,>=1.8.0
 Provides-Extra: torch
 Requires-Dist: torch >=2.2 ; extra == 'torch'
 

{dcnum-0.25.0.dist-info → dcnum-0.25.2.dist-info}/RECORD

@@ -1,5 +1,5 @@
 dcnum/__init__.py,sha256=hcawIKS7utYiOyVhOAX9t7K3xYzP1b9862VV0b6qSrQ,74
-dcnum/_version.py,sha256=nhq2LDshqyJE9A3DLIz_6mBkgGLKSQrYmHfzZ_jVCbc,413
+dcnum/_version.py,sha256=O16YsGa9nckhVhnz7jJ3nC69Kk6pQkIag-qsDHQCsBY,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
@@ -20,7 +20,7 @@ dcnum/feat/feat_texture/__init__.py,sha256=6StM9S540UVtdFFR3bHa7nfCTomeVdoo7Uy9C
 dcnum/feat/feat_texture/common.py,sha256=COXHpXS-7DMouGu3WF83I76L02Sr7P9re4lxajh6g0E,439
 dcnum/feat/feat_texture/tex_all.py,sha256=_5H3sXYRN0Uq2eUHn3XUyEHkU_tncEqbqJTC-HZcnGY,5198
 dcnum/logic/__init__.py,sha256=7J3GrwJInNQbrLk61HRIV7X7p69TAIbMYpR34hh6u14,177
-dcnum/logic/ctrl.py,sha256=3ovEkaxy4ASpXvLsZMO0pSueqZfQgLkoy3fnH2Gweq8,38791
+dcnum/logic/ctrl.py,sha256=FwzrCou4YBPBaaRRTqJkPt6jenFev9JfnxxjUMS0B-w,39042
 dcnum/logic/job.py,sha256=9BN2WjYqjjJuLnfNZAtQ2Nn47Glo2jVrivDodGJoqlQ,7713
 dcnum/logic/json_encoder.py,sha256=cxMnqisbKEVf-rVcw6rK2BBAb6iz_hKFaGl81kK36lQ,571
 dcnum/meta/__init__.py,sha256=AVqRgyKXO1orKnE305h88IBvoZ1oz6X11HN1WP5nGvg,60
@@ -47,10 +47,10 @@ dcnum/segm/segm_torch/torch_postproc.py,sha256=ctirQTmsZnuZGIxkwFWN9arRneHRYJUxa
 dcnum/segm/segm_torch/torch_preproc.py,sha256=kjabu76paw23kO7RP7Ik6IY60Kk1VBAHKBAedflA0aQ,4002
 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-0.25.0.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/write/queue_collector_thread.py,sha256=KwwNIDFEF2DU83woKES5K05MxxOhDxPMZLLeyPugfDo,11542
+dcnum/write/writer.py,sha256=oHlq4bDHQxb33-3Fw1xnzJwACecLyH-6koGK8SN0cSk,20528
+dcnum-0.25.2.dist-info/LICENSE,sha256=YRChA1C8A2E-amJbudwMcbTCZy_HzmeY0hMIvduh1MM,1089
+dcnum-0.25.2.dist-info/METADATA,sha256=8x1L3Y9upiMz-WC0GmOFYSkdcA9OMByyi2z88HRlX94,2326
+dcnum-0.25.2.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
+dcnum-0.25.2.dist-info/top_level.txt,sha256=Hmh38rgG_MFTVDpUDGuO2HWTSq80P585Het4COQzFTg,6
+dcnum-0.25.2.dist-info/RECORD,,

{dcnum-0.25.0.dist-info → dcnum-0.25.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (71.1.0)
+Generator: setuptools (74.1.2)
 Root-Is-Purelib: true
 Tag: py3-none-any