dclab 0.64.1__cp310-cp310-win_amd64.whl → 0.65.0__cp310-cp310-win_amd64.whl

dclab/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.64.1'
-__version_tuple__ = version_tuple = (0, 64, 1)
+__version__ = version = '0.65.0'
+__version_tuple__ = version_tuple = (0, 65, 0)

dclab/definitions/feat_logic.py

@@ -1,6 +1,11 @@
+import re
+
 from . import feat_const
 
 
+ML_SCORE_REGEX = re.compile(r"^ml_score_[a-z0-9]{3}$")
+
+
 def check_feature_shape(name, data):
     """Check if (non)-scalar feature matches with its data's dimensionality
 
@@ -17,11 +22,15 @@ def check_feature_shape(name, data):
         If the data's shape does not match its scalar description
     """
     if len(data.shape) == 1 and not scalar_feature_exists(name):
-        raise ValueError(f"Feature '{name}' is not a scalar feature, but "
-                         "a 1D array was given for `data`!")
+        raise ValueError(
+            f"Feature '{name}' is not a scalar feature, but "
+            "a 1D array was given for `data`!"
+        )
     elif len(data.shape) != 1 and scalar_feature_exists(name):
-        raise ValueError(f"Feature '{name}' is a scalar feature, but the "
-                         "`data` array is not 1D!")
+        raise ValueError(
+            f"Feature '{name}' is a scalar feature, but the "
+            "`data` array is not 1D!"
+        )
 
 
 def feature_exists(name, scalar_only=False):
@@ -56,15 +65,9 @@ def feature_exists(name, scalar_only=False):
     elif not scalar_only and name in feat_const.feature_names:
         # non-scalar feature
         valid = True
-    else:
-        # check whether we have an `ml_score_???` feature
-        valid_chars = "0123456789abcdefghijklmnopqrstuvwxyz"
-        if (name.startswith("ml_score_")
-            and len(name) == len("ml_score_???")
-            and name[-3] in valid_chars
-            and name[-2] in valid_chars
-                and name[-1] in valid_chars):
-            valid = True
+    elif ML_SCORE_REGEX.match(name):
+        # machine-learning score feature ml_score_???
+        valid = True
     return valid
 
 
@@ -93,8 +96,10 @@ def feature_register(name, label=None, is_scalar=True):
     allowed_chars = "abcdefghijklmnopqrstuvwxyz_1234567890"
     feat = "".join([f for f in name if f in allowed_chars])
     if feat != name:
-        raise ValueError("`feature` must only contain lower-case characters, "
-                         f"digits, and underscores; got '{name}'!")
+        raise ValueError(
+            "`feature` must only contain lower-case characters, "
+            f"digits, and underscores; got '{name}'!"
+        )
     if label is None:
         label = f"User-defined feature {name}"
     if feature_exists(name):
@@ -156,22 +161,16 @@ def get_feature_label(name, rtdc_ds=None, with_unit=True):
     TODO: extract feature label from ancillary information when an rtdc_ds is
     given.
     """
-    # TODO: Is there another way of avoiding this circular import?
-    from ..rtdc_dataset.feat_anc_core.ancillary_feature import AncillaryFeature
-    assert feature_exists(name)
     if name in feat_const.feature_name2label:
         label = feat_const.feature_name2label[name]
+    elif ML_SCORE_REGEX.match(name):
+        # use a generic name for machine-learning features
+        label = f"ML score {name[-3:].upper()}"
     else:
-        # First check whether an ancillary feature with that
-        # name exists.
-        for af in AncillaryFeature.features:
-            if af.feature_name == name:
-                labelid = af.data.outputs.index(name)
-                label = af.data.output_labels[labelid]
-                break
-        else:
-            # If that did not work, use a generic name.
-            label = "ML score {}".format(name[-3:].upper())
+        exists = feature_exists(name)
+        msg = f"Could not find label for '{name}'"
+        msg += " (feature does not exist)" if not exists else ""
+        raise ValueError(msg)
     if not with_unit:
         if label.endswith("]") and label.count("["):
             label = label.rsplit("[", 1)[0].strip()

dclab/rtdc_dataset/core.py

@@ -835,9 +835,9 @@ class RTDCBase(abc.ABC):
         identifier = self.config.get("experiment", {}).get("run identifier",
                                                            None)
         if identifier is None:
-            time = self.config.get("experiment", {}).get("time", None)
-            date = self.config.get("experiment", {}).get("date", None)
-            sid = self.config.get("setup", {}).get("identifier", None)
+            time = self.config.get("experiment", {}).get("time", None) or None
+            date = self.config.get("experiment", {}).get("date", None) or None
+            sid = self.config.get("setup", {}).get("identifier", None) or None
             if None not in [time, date, sid]:
                 # only compute an identifier if all of the above are defined.
                 hasher = hashlib.md5(f"{time}_{date}_{sid}".encode("utf-8"))

dclab/rtdc_dataset/export.py

@@ -334,8 +334,8 @@ class Export(object):
             # Define a new measurement identifier, so that we are not running
             # into any problems with basins being defined for filtered data.
             ds_run_id = ds.get_measurement_identifier()
-            random_ap = str(uuid.uuid4())[:4]
-            meta["experiment"]["run identifier"] = f"{ds_run_id}-{random_ap}"
+            random_ap = f"dclab-{str(uuid.uuid4())[:7]}"
+            meta["experiment"]["run identifier"] = f"{ds_run_id}_{random_ap}"
 
         if filtered:
             filter_arr = ds.filter.all

dclab/rtdc_dataset/feat_basin.py

@@ -458,22 +458,30 @@ class Basin(abc.ABC):
             if not self._measurement_identifier_verified:
                 if self.measurement_identifier is None:
                     # No measurement identifier was presented by the
-                    # referencing dataset. Don't perform any checks.
+                    # referencing dataset. We are in the dark.
+                    # Don't perform any checks.
                     self._measurement_identifier_verified = True
                 else:
-                    if self.mapping == "same":
-                        # When we have identical mapping, then the measurement
-                        # identifier has to match exactly.
-                        verifier = str.__eq__
+                    # This is the measurement identifier of the basin.
+                    basin_identifier = self.get_measurement_identifier()
+                    if basin_identifier is None:
+                        # Again, we are in the dark, because the basin dataset
+                        # does not have an identifier. This is an undesirable
+                        # situation, but there is nothing we can do about it.
+                        self._measurement_identifier_verified = True
                     else:
-                        # When we have non-identical mapping (e.g. exported
-                        # data), then the measurement identifier has to
-                        # partially match.
-                        verifier = str.startswith
-                    self._measurement_identifier_verified = verifier(
-                        self.measurement_identifier,
-                        self.get_measurement_identifier()
-                    )
+                        if self.mapping == "same":
+                            # When we have identical mapping, then the
+                            # measurement identifier has to match exactly.
+                            verifier = str.__eq__
+                        else:
+                            # When we have non-identical mapping (e.g. exported
+                            # data), then the measurement identifier has to
+                            # partially match.
+                            verifier = str.startswith
+                        self._measurement_identifier_verified = verifier(
+                            self.measurement_identifier, basin_identifier)
+
             check_rid = self._measurement_identifier_verified
         else:
             check_rid = True
@@ -538,8 +546,12 @@ class BasinProxy:
 
     def __getitem__(self, feat):
         if feat not in self._features:
-            feat_obj = BasinProxyFeature(feat_obj=self.ds[feat],
-                                         basinmap=self.basinmap)
+            if feat == "contour":
+                raise NotImplementedError("Feature 'contour' cannot be "
+                                          "handled by BasinProxy.")
+            else:
+                feat_obj = BasinProxyFeature(feat_obj=self.ds[feat],
+                                             basinmap=self.basinmap)
             self._features[feat] = feat_obj
         return self._features[feat]
 

{dclab-0.64.1.dist-info → dclab-0.65.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dclab
-Version: 0.64.1
+Version: 0.65.0
 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-0.64.1.dist-info → dclab-0.65.0.dist-info}/RECORD

@@ -1,7 +1,7 @@
 dclab/__init__.py,sha256=kSr6VI0UI-beS9beOEpERTUAV1NINHx_G6u1VmBm9D8,1624
-dclab/_version.py,sha256=mXVRd4XXSvubXnCvvibtN_3CiyIT4FFBF_TNPrxM6fk,534
+dclab/_version.py,sha256=_mxGrRjXWiOF95UUEGVhRBBil-513LRs9VvSfA91XWs,534
 dclab/cached.py,sha256=t01BYTf43VEsBYa0c-bMxgceF5vKoGV73b42UlLH6Lo,3014
-dclab/downsampling.cp310-win_amd64.pyd,sha256=X_wo94A8SQfEmWuhPDdUtufM1fottem5gya-sVZJB1U,171008
+dclab/downsampling.cp310-win_amd64.pyd,sha256=C4wSBuvQLqGUfuDmdiHKBTbGsN-oF9mQ5Cp4ybo3uao,174080
 dclab/downsampling.pyx,sha256=Ez6MbNbzCUzs2IXXKtAYsjtYqP22kI8hdA1IE-3mqvY,7488
 dclab/http_utils.py,sha256=aIW4ATmyk02AjQmoTm7mAWdsaQD1siEPLx47IlEcYls,11234
 dclab/kde_contours.py,sha256=cYeBtvbBqLHCz5W8AiEAAd9O3yLsSBbLcRVj1WZ1pRo,288
@@ -21,7 +21,7 @@ dclab/cli/task_tdms2rtdc.py,sha256=5YjDCLl9NoZMbeZtl7csH5qx_8dvzF3p-8ndsneOhBI,8
 dclab/cli/task_verify_dataset.py,sha256=OFy7aWHvA6NInndnMBg0MVZSBibvJeNHhc_C79_9PAk,2780
 dclab/definitions/__init__.py,sha256=cubgnqpBbPgk_c1_uUPggRsmtUd-baV1haybLqbMf8k,2860
 dclab/definitions/feat_const.py,sha256=I772sd6aSNv8PzhT9MHnNKbGhx6ZJt3z3_FVs5oxMtw,9836
-dclab/definitions/feat_logic.py,sha256=uMHXInzESTtBWPBsk9PxqSFFrSM1vNbTDxOlso9zhT0,6006
+dclab/definitions/feat_logic.py,sha256=ZZlf3-uze5qFvRtlTHJQZmE9mTF3L7TMyk8YTnCCRzw,5561
 dclab/definitions/meta_const.py,sha256=X3U3orhlY_i78TYN4DUBJaOGBltNnXaRsQauH1LxuJ0,13377
 dclab/definitions/meta_logic.py,sha256=no6fTCmKFrwpmirs_9358-Ysh5aZeib1xJrL_30WkqU,4305
 dclab/definitions/meta_parse.py,sha256=UtgSm7hkfqnyj6FAbDmctbXqfZOHU9d4uoMf3EcYWtQ,2487
@@ -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.cp310-win_amd64.pyd,sha256=6LBeM0ouF9VKNYJAjZqRcGuskDkq1VF2l0jd8p6q6b0,130560
+dclab/external/skimage/_find_contours_cy.cp310-win_amd64.pyd,sha256=05dRdui2WfHhrDA1LjcOgq50458ezuqqQ_TlASgwUnY,136704
 dclab/external/skimage/_find_contours_cy.pyx,sha256=c-EobLhKjZNCpuqWxmvrcH35uAY_Bu-_hZiUHbXODms,7349
-dclab/external/skimage/_pnpoly.cp310-win_amd64.pyd,sha256=cirbA6YjChDalZ5qb-t3cRQqLCUrTpqrJBAuGtPXXjc,145408
+dclab/external/skimage/_pnpoly.cp310-win_amd64.pyd,sha256=TcwABtRSlww31gsxwYGI-hMoUZm8hWFl_yCNlEDFqIY,150016
 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.cp310-win_amd64.pyd,sha256=_tbxPCmes67nhMOcW1-PA-XZdk4ffiglrgDVBwP12r0,19456
+dclab/external/skimage/_shared/geometry.cp310-win_amd64.pyd,sha256=wfOnppHCysMnJF2X3RjNy38znrsHRJjMGwqzpq4FAHI,19968
 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
@@ -87,9 +87,9 @@ dclab/rtdc_dataset/__init__.py,sha256=BuWKEUm7QUe-Kj1wMR0AXON_XN2mzXlbOgouHdnvAw
 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=imD0ijAz9BY0nksF2zUBeoGmeo_dUTUnBgY9TqRaD4g,14528
-dclab/rtdc_dataset/core.py,sha256=qbxcCBJOSb8433CEnTGaYTw5OeSDZNDL22rc9UlPXyg,35647
-dclab/rtdc_dataset/export.py,sha256=zY88vbIJvO6duqrjzrUboa0WnFI0fEf3cao_0x7Qyfk,34250
-dclab/rtdc_dataset/feat_basin.py,sha256=Q7Eqt9iyNh-ooXLOb3IUXEu5UgkYq4m5jj5VOViJFAo,26857
+dclab/rtdc_dataset/core.py,sha256=jOE21lhOC3ViA68QiykGVOs437SlCotTYRTcA9Tk2MQ,35671
+dclab/rtdc_dataset/export.py,sha256=tjJjP9Scg-ak0fI7wmmRuFEm4-h_1fkj9N6__VF8P44,34261
+dclab/rtdc_dataset/feat_basin.py,sha256=nMDw5T_lvhbllG1SmCy6dBrOc5yeNp7eX0uWyTTE1tY,27618
 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
@@ -134,9 +134,9 @@ 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-0.64.1.dist-info/licenses/LICENSE,sha256=Aq3cYb2xLk3Y_aIOhaoZxi8FlVeMVs3-3FMEBvAEixM,15643
-dclab-0.64.1.dist-info/METADATA,sha256=g2ygLFICqk7MKmTDzdSZIdHfR4YVuCpqytG8HSy69qo,4913
-dclab-0.64.1.dist-info/WHEEL,sha256=KUuBC6lxAbHCKilKua8R9W_TM71_-9Sg5uEP3uDWcoU,101
-dclab-0.64.1.dist-info/entry_points.txt,sha256=eOpjgznu-eW-9utUpLU-77O5098YyUEgGF3ksGMdtec,273
-dclab-0.64.1.dist-info/top_level.txt,sha256=irvwZMgs1edY1Zj60ZFk7Almb9Zhk4k6E6aC4YPFnnM,6
-dclab-0.64.1.dist-info/RECORD,,
+dclab-0.65.0.dist-info/licenses/LICENSE,sha256=Aq3cYb2xLk3Y_aIOhaoZxi8FlVeMVs3-3FMEBvAEixM,15643
+dclab-0.65.0.dist-info/METADATA,sha256=uAUuKYkN9sH3Ii8cZsuM4bc5cL4p8ssKpTMZKFao00E,4913
+dclab-0.65.0.dist-info/WHEEL,sha256=KUuBC6lxAbHCKilKua8R9W_TM71_-9Sg5uEP3uDWcoU,101
+dclab-0.65.0.dist-info/entry_points.txt,sha256=eOpjgznu-eW-9utUpLU-77O5098YyUEgGF3ksGMdtec,273
+dclab-0.65.0.dist-info/top_level.txt,sha256=irvwZMgs1edY1Zj60ZFk7Almb9Zhk4k6E6aC4YPFnnM,6
+dclab-0.65.0.dist-info/RECORD,,