dclab 0.62.8__cp39-cp39-win_amd64.whl → 0.62.10__cp39-cp39-win_amd64.whl

dclab/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.62.8'
-__version_tuple__ = version_tuple = (0, 62, 8)
+__version__ = version = '0.62.10'
+__version_tuple__ = version_tuple = (0, 62, 10)

dclab/rtdc_dataset/copier.py

@@ -178,42 +178,51 @@ def basin_definition_copy(src_h5file, dst_h5file, features_iter):
     relevant for the internal basin.
     """
     dst_h5file.require_group("basins")
-    for b_key in src_h5file["basins"]:
+    # Load the basin information
+    basin_dicts = RTDC_HDF5.basin_get_dicts_from_h5file(src_h5file)
+    for bn in basin_dicts:
+        b_key = bn["key"]
+
         if b_key in dst_h5file["basins"]:
-            # This basin already exists.
+            # already stored therein
             continue
-        # Load the basin information
-        basin_dicts = RTDC_HDF5.basin_get_dicts_from_h5file(src_h5file)
-        for bn in basin_dicts:
-            if bn["type"] == "internal":
-                # Make sure we define the internal features selected
-                feat_used = [f for f in bn["features"] if f in features_iter]
-                if len(feat_used) == 0:
-                    # We don't have any internal features, don't write anything
-                    continue
-                elif feat_used != bn["features"]:
-                    bn["features"] = feat_used
-                    rewrite = True
-                else:
-                    rewrite = False
+
+        # sanity check
+        if b_key not in src_h5file["basins"]:
+            raise ValueError(
+                f"Failed to parse basin information correctly. Source file "
+                f"{src_h5file} does not contain basin {b_key} which I got "
+                f"from `RTDC_HDF5.basin_get_dicts_from_h5file`.")
+
+        if bn["type"] == "internal":
+            # Make sure we define the internal features selected
+            feat_used = [f for f in bn["features"] if f in features_iter]
+            if len(feat_used) == 0:
+                # We don't have any internal features, don't write anything
+                continue
+            elif feat_used != bn["features"]:
+                bn["features"] = feat_used
+                rewrite = True
             else:
-                # We do not have an internal basin, just copy everything
                 rewrite = False
+        else:
+            # We do not have an internal basin, just copy everything
+            rewrite = False
 
-            if rewrite:
-                # Convert edited `bn` to JSON and write feature data
-                b_lines = json.dumps(bn, indent=2).split("\n")
-                key = hashobj(b_lines)
-                if key not in dst_h5file["basins"]:
-                    with RTDCWriter(dst_h5file) as hw:
-                        hw.write_text(dst_h5file["basins"], key, b_lines)
-            else:
-                # copy only
-                h5ds_copy(src_loc=src_h5file["basins"],
-                          src_name=b_key,
-                          dst_loc=dst_h5file["basins"],
-                          dst_name=b_key,
-                          recursive=False)
+        if rewrite:
+            # Convert edited `bn` to JSON and write feature data
+            b_lines = json.dumps(bn, indent=2).split("\n")
+            key = hashobj(b_lines)
+            if key not in dst_h5file["basins"]:
+                with RTDCWriter(dst_h5file) as hw:
+                    hw.write_text(dst_h5file["basins"], key, b_lines)
+        else:
+            # copy only
+            h5ds_copy(src_loc=src_h5file["basins"],
+                      src_name=b_key,
+                      dst_loc=dst_h5file["basins"],
+                      dst_name=b_key,
+                      recursive=False)
 
 
 def h5ds_copy(src_loc, src_name, dst_loc, dst_name=None,

dclab/rtdc_dataset/core.py

@@ -1,6 +1,7 @@
 """RT-DC dataset core classes and methods"""
 import abc
 import hashlib
+import json
 import os.path
 import pathlib
 import traceback
@@ -15,6 +16,7 @@ from .. import definitions as dfn
 from .. import downsampling
 from ..polygon_filter import PolygonFilter
 from .. import kde_methods
+from ..util import hashobj
 
 from .feat_anc_core import AncillaryFeature, FEATURES_RAPID
 from . import feat_basin
@@ -825,14 +827,20 @@ class RTDCBase(abc.ABC):
         # Sort basins according to priority
         bdicts_srt = sorted(self.basins_get_dicts(),
                             key=feat_basin.basin_priority_sorted_key)
-        bd_keys = [bd["key"] for bd in bdicts_srt if "key" in bd]
+        # complement basin "key"s (we do the same in writer)
+        for bdict in bdicts_srt:
+            if "key" not in bdict:
+                b_dat = json.dumps(bdict, indent=2, sort_keys=True).split("\n")
+                bdict["key"] = hashobj(b_dat)
+
+        bd_keys = [bd["key"] for bd in bdicts_srt]
         bd_keys += self._basins_ignored
         for bdict in bdicts_srt:
             if bdict["format"] not in bc:
                 warnings.warn(f"Encountered unsupported basin "
                               f"format '{bdict['format']}'!")
                 continue
-            if "key" in bdict and bdict["key"] in self._basins_ignored:
+            if bdict["key"] in self._basins_ignored:
                 warnings.warn(
                     f"Encountered cyclic basin dependency '{bdict['key']}'",
                     feat_basin.CyclicBasinDependencyFoundWarning)
@@ -853,6 +861,8 @@ class RTDCBase(abc.ABC):
                 "measurement_identifier": self.get_measurement_identifier(),
                 # allow to ignore basins
                 "ignored_basins": bd_keys,
+                # basin key
+                "key": bdict["key"],
             }
 
             # Check whether this basin is supported and exists

dclab/rtdc_dataset/export.py

@@ -319,18 +319,21 @@ class Export(object):
 
             # write export log
             hw.store_log(time.strftime("dclab-export_%Y-%m-%d_%H.%M.%S"),
-                         json.dumps({
-                             "dclab version": version_tuple,
-                             "kwargs": {
-                                 "features": features,
-                                 "filtered": filtered,
-                                 "logs": logs,
-                                 "tables": tables,
-                                 "basins": basins,
-                                 "meta_prefix": meta_prefix,
-                                 "skip_checks": skip_checks
-                             }
-                         }).split("\n"))
+                         json.dumps(
+                             {"dclab version": version_tuple,
+                              "kwargs": {
+                                  "features": features,
+                                  "filtered": filtered,
+                                  "logs": logs,
+                                  "tables": tables,
+                                  "basins": basins,
+                                  "meta_prefix": meta_prefix,
+                                  "skip_checks": skip_checks
+                                  }
+                              },
+                             indent=2,
+                             sort_keys=True,
+                         ).split("\n"))
 
             if logs:
                 # write logs

dclab/rtdc_dataset/feat_basin.py

@@ -9,6 +9,7 @@ import abc
 import numbers
 import threading
 from typing import Dict, List, Literal
+import uuid
 import warnings
 import weakref
 
@@ -74,6 +75,7 @@ class Basin(abc.ABC):
                                   ] = "same",
                  mapping_referrer: Dict = None,
                  ignored_basins: List[str] = None,
+                 key: str = None,
                  **kwargs):
         """
 
@@ -109,6 +111,10 @@ class Basin(abc.ABC):
             :class:`.RTDCBase`.
         ignored_basins: list of str
             List of basins to ignore in subsequent basin instantiations
+        key: str
+            Unique key to identify this basin; normally computed from
+            a JSON dump of the basin definition. A random string is used
+            if None is specified.
         kwargs:
             Additional keyword arguments passed to the `load_dataset`
             method of the `Basin` subclass.
@@ -124,6 +130,8 @@ class Basin(abc.ABC):
         self.name = name
         #: lengthy description of the basin
         self.description = description
+        # defining key of the basin
+        self.key = key or str(uuid.uuid4())
         # features this basin provides
         self._features = features
         #: measurement identifier of the referencing dataset
@@ -367,6 +375,7 @@ class BasinProxy:
             dataset to the downstream dataset
         """
         self.ds = ds
+        self.basins_get_dicts = ds.basins_get_dicts
         self.basinmap = basinmap
         self._features = {}
 

dclab/rtdc_dataset/writer.py

@@ -389,7 +389,7 @@ class RTDCWriter:
                     flocs.append(str(pp.resolve()))
                     # Also store the relative path for user convenience.
                     # Don't use pathlib.Path.relative_to, because that
-                    # is deprecated in Python 3.12.
+                    # only has `walk_up` since Python 3.12.
                     # Also, just look in subdirectories which simplifies
                     # path resolution.
                     this_parent = str(self.path.parent) + os.sep
@@ -408,7 +408,7 @@ class RTDCWriter:
         else:
             raise ValueError(f"Unknown basin type '{basin_type}'")
 
-        b_lines = json.dumps(b_data, indent=2).split("\n")
+        b_lines = json.dumps(b_data, indent=2, sort_keys=True).split("\n")
         basins = self.h5file.require_group("basins")
         key = hashobj(b_lines)
         if key not in basins:

{dclab-0.62.8.dist-info → dclab-0.62.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dclab
-Version: 0.62.8
+Version: 0.62.10
 Summary: Library for real-time deformability cytometry (RT-DC)
 Author: Benedikt Hartmann, Eoghan O'Connell, Maik Herbig, Maximilian Schlögel, Nadia Sbaa, Paul Müller, Philipp Rosendahl, Raghava Alajangi
 Maintainer-email: Paul Müller <dev@craban.de>

{dclab-0.62.8.dist-info → dclab-0.62.10.dist-info}/RECORD

@@ -1,7 +1,7 @@
 dclab/__init__.py,sha256=7_y6YtYcoL_a5M6Q9PiwZPzHSxS66yCTgs_uuK5C1dg,835
-dclab/_version.py,sha256=qVziVuodFeRMjE4HHLtmm_Yy49iMpeo90iqYHmVvyE0,429
+dclab/_version.py,sha256=24GJ4WG-lYF3ho697oXBQgdaa52ggyKu0hOZMiA4lV8,431
 dclab/cached.py,sha256=t01BYTf43VEsBYa0c-bMxgceF5vKoGV73b42UlLH6Lo,3014
-dclab/downsampling.cp39-win_amd64.pyd,sha256=plPfBj6ljqUvfb182t73jnAmhLkkwaMFnOlYRzclhPs,187904
+dclab/downsampling.cp39-win_amd64.pyd,sha256=M2HpYHQmcWc-BSswv93slyWZDyWnzZkW9FUZ9mrVv-Y,187904
 dclab/downsampling.pyx,sha256=Ez6MbNbzCUzs2IXXKtAYsjtYqP22kI8hdA1IE-3mqvY,7488
 dclab/http_utils.py,sha256=nneq9Cx8dw8ChQx5oIg2pN0xGkvNWCMSY5VYmttqyXA,11232
 dclab/kde_contours.py,sha256=k0Y1UsJNtuYY8iqYmfQ-Nml-dFpJAcigd3vmt9U6zsY,6967
@@ -35,14 +35,14 @@ dclab/external/packaging/version.py,sha256=NgEgv7me4UCvFMyiNYD-nc_28b9UHUvBVh8RD
 dclab/external/skimage/LICENSE,sha256=Tdv08zzxYV32WRdYnco9P3nVyS5w17OTxIAFeRSd1wc,1480
 dclab/external/skimage/__init__.py,sha256=icOIlThkyn_hxmnM_i7OpbU7fhvqYWNpGdNGD38qthU,74
 dclab/external/skimage/_find_contours.py,sha256=auRMNfZg7B73DX7kPXxgD8gMXXB3Lk9QDWt4wlQnUWg,9556
-dclab/external/skimage/_find_contours_cy.cp39-win_amd64.pyd,sha256=MPdRf81FeTfdEBW_jcNo5eFavT4AsJu_5IZsS9Lu9fc,142848
+dclab/external/skimage/_find_contours_cy.cp39-win_amd64.pyd,sha256=9NGAQ_vlN6Ol2huZJLO9oxYHvu2hwtagDlXikgi_t0I,142848
 dclab/external/skimage/_find_contours_cy.pyx,sha256=c-EobLhKjZNCpuqWxmvrcH35uAY_Bu-_hZiUHbXODms,7349
-dclab/external/skimage/_pnpoly.cp39-win_amd64.pyd,sha256=ISMtCHcUrgszeXwsXEVOPD2i21X8CKxZUEc3glM0mvw,159232
+dclab/external/skimage/_pnpoly.cp39-win_amd64.pyd,sha256=1w_8E7qR3bXJIO1Wld6Ltr-3pQYGWHaplJuEvWHEt7k,159232
 dclab/external/skimage/_pnpoly.pyx,sha256=eHV3DlIGcBhAQ12-Y58EYq8xcq0Sibyc4xTxzX9NJsk,2603
 dclab/external/skimage/measure.py,sha256=rzyI0HCr9O9GJNieVW8pcqDjTGRAdSehDUawD8QkIAE,254
 dclab/external/skimage/pnpoly.py,sha256=zB4rSxjHJyY1OsGZ7QfFQqxIEDLGK8CWPehwutoFqm4,1400
 dclab/external/skimage/_shared/__init__.py,sha256=q29esTsNh0HfQxcd2EuwdYNbEBJwo_qY4dfv7RihzoA,38
-dclab/external/skimage/_shared/geometry.cp39-win_amd64.pyd,sha256=8FS3FXh84_YmsAxKOJvMN5P6SucGxYackdnH_8MvnHw,21504
+dclab/external/skimage/_shared/geometry.cp39-win_amd64.pyd,sha256=7oIlbpGgB1Dm13DHRI6IAO3KbjrSJ93PNUQIfrLVJq4,21504
 dclab/external/skimage/_shared/geometry.pxd,sha256=3gJ7fbXXsxJunSN4biE0dzEbZpX9ZqzR4cUDDN0JnAU,352
 dclab/external/skimage/_shared/geometry.pyx,sha256=b6hADE8chse63haO1Kdt13_oQ54J9tkBf7dVA22-s-M,1722
 dclab/external/statsmodels/LICENSE,sha256=8D7nwukc6YgsZCdN9mG0psM3I9j-z8fuUgFyVhnMXpU,1672
@@ -82,17 +82,17 @@ dclab/lme4/wrapr.py,sha256=tZYvUy5LUM7sM3d8NiOIlxbrtu89LAihG4hqI6MSv2Q,15403
 dclab/rtdc_dataset/__init__.py,sha256=BuWKEUm7QUe-Kj1wMR0AXON_XN2mzXlbOgouHdnvAw4,501
 dclab/rtdc_dataset/check.py,sha256=l2QoIL3gno_Z2-e8RvYHAurHZP_oLGtZk8l6jUDiuTA,35908
 dclab/rtdc_dataset/config.py,sha256=HVJiqKlqd-SpYqnNTKSr1yUsq2Bkfq5s5zluT-8PUc0,17965
-dclab/rtdc_dataset/copier.py,sha256=f8ySDHnuSWfZYI_kPCCrzickTOo6NqovBGvzMTCbK4M,14339
-dclab/rtdc_dataset/core.py,sha256=yTxpOPqb6Ihaqmq5wJLRtkxHzpPQNUN3O3DyOw0dZJ4,38663
-dclab/rtdc_dataset/export.py,sha256=iqWzj9BjPVhs-d3898DLM9y5rLxTSIaN0S3po42IPdU,30219
-dclab/rtdc_dataset/feat_basin.py,sha256=Gi9Ct5TRABieacG5fVMONBocVbik_D5p6Ii1NYNdgVM,21241
+dclab/rtdc_dataset/copier.py,sha256=imD0ijAz9BY0nksF2zUBeoGmeo_dUTUnBgY9TqRaD4g,14528
+dclab/rtdc_dataset/core.py,sha256=7pQOcFGEO2AnI7r8rJLjXkAi8mXkY4GCQ41eXfBHMx0,38999
+dclab/rtdc_dataset/export.py,sha256=gdcg8FSacFBdIfCPbquEOV7J96FlHAvWu9PpK2KTdkc,30351
+dclab/rtdc_dataset/feat_basin.py,sha256=nDMMkjBmVrH26_lhSJ4pmgUfcwdV1wDON-Hu-864is8,21622
 dclab/rtdc_dataset/feat_temp.py,sha256=5QiF8Nc8MVoTtinYlvfoSuoopND-uvWVWKjMggBTHLw,3796
 dclab/rtdc_dataset/filter.py,sha256=IRaEUt0tWtZGLKYvtqzfYO2kN5yhqx9eLoHd3VOLCTE,10286
 dclab/rtdc_dataset/fmt_dict.py,sha256=-tlzOwsOCh4Vt3rSiBUvMKW7vBgrRNubU7ZHdGMB3gE,3112
 dclab/rtdc_dataset/fmt_http.py,sha256=XzcgvJ4lm-eWbveBraBc5PPJeGWeUGC35p8ptnxBycc,3476
 dclab/rtdc_dataset/fmt_s3.py,sha256=35ZNCSbfpn75QHqrciMur2MUAiViddCAZsXkzql6uv0,10962
 dclab/rtdc_dataset/load.py,sha256=IKRtlZbHGAHNCNaZQPRXFxJjnnMH5HXnhNuIwqYmHzo,2545
-dclab/rtdc_dataset/writer.py,sha256=Actk8Xan-TbZEOQs0joLf5IBMvfwMw7JFlfkiTi2aPQ,41393
+dclab/rtdc_dataset/writer.py,sha256=f4xU55FvxJEoxwzjqEQzXrlr1eZe3PFaprh_8g4qyf8,41417
 dclab/rtdc_dataset/feat_anc_core/__init__.py,sha256=j7vtbQGJid3hchXryo19cxnwanepdDQ_RuJVf740mZs,488
 dclab/rtdc_dataset/feat_anc_core/af_basic.py,sha256=7pM6Gn1ZkuttHNfkaLijPudddAu0jMDPGJS9HzKh8rE,2268
 dclab/rtdc_dataset/feat_anc_core/af_emodulus.py,sha256=lsJpQ409EsxnMtyhO7igquWnJxIhXz_w9f8vtIq7F1M,6830
@@ -129,9 +129,9 @@ dclab/rtdc_dataset/fmt_tdms/event_mask.py,sha256=cW-Tw2PIe6X1Hc4UZJ22-mI_qFaIMWA
 dclab/rtdc_dataset/fmt_tdms/event_trace.py,sha256=ktWnXfMir1v5Wfeo7tOd0txSOe1bgsXotf9Ul5T5-B4,5361
 dclab/rtdc_dataset/fmt_tdms/exc.py,sha256=FfxUY4LGIMPGJTYmGITmEm7X5iu8GBsj7OfZR8Zb-IE,850
 dclab/rtdc_dataset/fmt_tdms/naming.py,sha256=SFeWiwIN7sg0qNe0Aya2bZshN1Zbw4YcOKunZ6kfIGM,5524
-dclab-0.62.8.dist-info/LICENSE,sha256=ayjnuJcdf_kpkDyD61tUcVqVAQaNSYXJ73m5HVB4G8s,18474
-dclab-0.62.8.dist-info/METADATA,sha256=XEPR3tgdPJL4PXaajLI_JCjmeYH0H9Zlf91vRVluadc,4900
-dclab-0.62.8.dist-info/WHEEL,sha256=EfPXSsrLwp9clrn29v9vbmPfEm-IfFzseSJd0ZtI9XA,99
-dclab-0.62.8.dist-info/entry_points.txt,sha256=eOpjgznu-eW-9utUpLU-77O5098YyUEgGF3ksGMdtec,273
-dclab-0.62.8.dist-info/top_level.txt,sha256=irvwZMgs1edY1Zj60ZFk7Almb9Zhk4k6E6aC4YPFnnM,6
-dclab-0.62.8.dist-info/RECORD,,
+dclab-0.62.10.dist-info/LICENSE,sha256=ayjnuJcdf_kpkDyD61tUcVqVAQaNSYXJ73m5HVB4G8s,18474
+dclab-0.62.10.dist-info/METADATA,sha256=BK3yCJmIW35QfOANM9-gPElFn5cnwWw7Tqj_Mm3D70Q,4901
+dclab-0.62.10.dist-info/WHEEL,sha256=F4Gwseysu0orsWha5ii3stWN2C03NSU54-GIdk79KZs,99
+dclab-0.62.10.dist-info/entry_points.txt,sha256=eOpjgznu-eW-9utUpLU-77O5098YyUEgGF3ksGMdtec,273
+dclab-0.62.10.dist-info/top_level.txt,sha256=irvwZMgs1edY1Zj60ZFk7Almb9Zhk4k6E6aC4YPFnnM,6
+dclab-0.62.10.dist-info/RECORD,,

{dclab-0.62.8.dist-info → dclab-0.62.10.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (75.7.0)
 Root-Is-Purelib: false
 Tag: cp39-cp39-win_amd64