dclab 0.62.9__cp38-cp38-win_amd64.whl → 0.62.11__cp38-cp38-win_amd64.whl

dclab/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.62.9'
-__version_tuple__ = version_tuple = (0, 62, 9)
+__version__ = version = '0.62.11'
+__version_tuple__ = version_tuple = (0, 62, 11)

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/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/fmt_dcor/tables.py

@@ -30,11 +30,13 @@ class DCORTables:
             tables = {}
             for key in table_data:
                 columns, data = table_data[key]
-                ds_dt = np.dtype({'names': columns,
-                                  'formats': [np.float64] * len(columns)})
                 tab_data = np.asarray(data)
-                rec_arr = np.rec.array(tab_data, dtype=ds_dt)
-                tables[key] = rec_arr
+                if columns is not None:
+                    # We have a rec-array (named columns)
+                    ds_dt = np.dtype({'names': columns,
+                                      'formats': [np.float64] * len(columns)})
+                    tab_data = np.rec.array(tab_data, dtype=ds_dt)
+                tables[key] = tab_data
 
             self._tables_cache = tables
         return self._tables_cache

dclab/rtdc_dataset/writer.py

@@ -616,7 +616,7 @@ class RTDCWriter:
                     convfunc = dfn.get_config_value_func(sec, ck)
                     self.h5file.attrs[idk] = convfunc(value)
 
-    def store_table(self, name, cmp_array):
+    def store_table(self, name, cmp_array, h5_attrs=None):
         """Store a compound array table
 
         Tables are semi-metadata. They may contain information collected
@@ -629,16 +629,33 @@ class RTDCWriter:
         ----------
         name: str
             Name of the table
-        cmp_array: np.recarray, h5py.Dataset, or dict
+        cmp_array: np.recarray, h5py.Dataset, np.ndarray, or dict
             If a np.recarray or h5py.Dataset are provided, then they
             are written as-is to the file. If a dictionary is provided,
             then the dictionary is converted into a numpy recarray.
+            If a numpy array is provided, then the array is written
+            as a raw table (no column names) to the file.
+        h5_attrs: dict, optional
+            Attributes to store alongside the corresponding HDF5 dataset
         """
-        if isinstance(cmp_array, (np.recarray, h5py.Dataset)):
+        if h5_attrs is None:
+            h5_attrs = {}
+
+        if isinstance(cmp_array, np.recarray):
             # A table is a compound array (np.recarray). If we are here,
-            # this means that the user passed an instance of np.recarray
-            # or an instance h5py.Dataset (which we trust to be a proper
+            # this means that the user passed an instance of np.recarray.
+            pass
+        elif isinstance(cmp_array, h5py.Dataset):
+            # An instance of h5py.Dataset (which we trust to be a proper
             # compound dataset at this point). No additional steps needed.
+            h5_attrs.update(cmp_array.attrs)
+            pass
+        elif isinstance(cmp_array, np.ndarray):
+            # A numpy array was passed. This usually means we have something
+            # that we can look at, so we add image tags.
+            h5_attrs['CLASS'] = np.bytes_('IMAGE')
+            h5_attrs['IMAGE_VERSION'] = np.bytes_('1.2')
+            h5_attrs['IMAGE_SUBCLASS'] = np.bytes_('IMAGE_GRAYSCALE')
             pass
         elif isinstance(cmp_array, dict):
             # The user passed a dict which we now have to convert to a
@@ -659,16 +676,18 @@ class RTDCWriter:
         else:
             raise NotImplementedError(
                 f"Cannot convert {type(cmp_array)} to table!")
+
+        # data
         group = self.h5file.require_group("tables")
         tab = group.create_dataset(
             name,
             data=cmp_array,
             fletcher32=True,
             **self.compression_kwargs)
-        # Also store metadata
-        if hasattr(cmp_array, "attrs"):
-            for key in cmp_array.attrs:
-                tab.attrs[key] = cmp_array.attrs[key]
+
+        # metadata
+        if h5_attrs:
+            tab.attrs.update(h5_attrs)
 
     def version_brand(self, old_version=None, write_attribute=True):
         """Perform version branding

{dclab-0.62.9.dist-info → dclab-0.62.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dclab
-Version: 0.62.9
+Version: 0.62.11
 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-0.62.9.dist-info → dclab-0.62.11.dist-info}/RECORD

@@ -1,7 +1,7 @@
 dclab/__init__.py,sha256=7_y6YtYcoL_a5M6Q9PiwZPzHSxS66yCTgs_uuK5C1dg,835
-dclab/_version.py,sha256=NL_KF0HMvQA9ov7bA-jEvOCXhXF0zvRwnc5Mbv4n8RM,429
+dclab/_version.py,sha256=6k5Rk2Ap5YBUoGawDNLFVJOIfoIxcLr4FCtSHL8cFtM,431
 dclab/cached.py,sha256=t01BYTf43VEsBYa0c-bMxgceF5vKoGV73b42UlLH6Lo,3014
-dclab/downsampling.cp38-win_amd64.pyd,sha256=XQU_KjcUsxy_JnqR-tw2R6V7jqBHC6aQ37mo-1Csj40,188416
+dclab/downsampling.cp38-win_amd64.pyd,sha256=Cja8o_nAfEghPl5QWchDSeo0XHR3BjrEVR7vBK9awTA,188416
 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.cp38-win_amd64.pyd,sha256=w1ki1KOaPiGNx2YdWm2O5fSRGj9jUFaIV1CATKpErDU,143360
+dclab/external/skimage/_find_contours_cy.cp38-win_amd64.pyd,sha256=qI8cmG0oKKLnp4X1zdWasThrkvlYcdvUWkaYeHQEIv4,143360
 dclab/external/skimage/_find_contours_cy.pyx,sha256=c-EobLhKjZNCpuqWxmvrcH35uAY_Bu-_hZiUHbXODms,7349
-dclab/external/skimage/_pnpoly.cp38-win_amd64.pyd,sha256=wp6bA4-bCIzfjzvBP1AvT9a5JbOIpAgOg7QJySzPke4,159232
+dclab/external/skimage/_pnpoly.cp38-win_amd64.pyd,sha256=sfQRn1BbmMQbUEq5tA8aTZHoKQJSLAdKLTgBFfaIHfk,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.cp38-win_amd64.pyd,sha256=yH5tAYkqm75XVjR9I8Wrsv_KUevp4eYHE5885yyb_js,21504
+dclab/external/skimage/_shared/geometry.cp38-win_amd64.pyd,sha256=ir0LVlLVx0sHKIO8PDHK-37vFfCoija2Tm-eZpxQ9TM,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
@@ -82,9 +82,9 @@ 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/copier.py,sha256=imD0ijAz9BY0nksF2zUBeoGmeo_dUTUnBgY9TqRaD4g,14528
 dclab/rtdc_dataset/core.py,sha256=7pQOcFGEO2AnI7r8rJLjXkAi8mXkY4GCQ41eXfBHMx0,38999
-dclab/rtdc_dataset/export.py,sha256=iqWzj9BjPVhs-d3898DLM9y5rLxTSIaN0S3po42IPdU,30219
+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
@@ -92,7 +92,7 @@ dclab/rtdc_dataset/fmt_dict.py,sha256=-tlzOwsOCh4Vt3rSiBUvMKW7vBgrRNubU7ZHdGMB3g
 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=f4xU55FvxJEoxwzjqEQzXrlr1eZe3PFaprh_8g4qyf8,41417
+dclab/rtdc_dataset/writer.py,sha256=IWD4hepdcF-x0fTe_90WQuOu0XEZ4UQ2kcPhWg05xI4,42157
 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
@@ -109,7 +109,7 @@ dclab/rtdc_dataset/fmt_dcor/api.py,sha256=v7xAxZtjPpQiSRq9AgYhrV6I9iM7KpPv38WzSE
 dclab/rtdc_dataset/fmt_dcor/base.py,sha256=i9VWbKtPlY3K1WeFll3iAKXEhznVvJjQE1jVaEM2c9g,6788
 dclab/rtdc_dataset/fmt_dcor/basin.py,sha256=JzofdU45r-TTBGl8Nnvo-j-YsnT23X2gXnvaOSINJxg,2599
 dclab/rtdc_dataset/fmt_dcor/logs.py,sha256=e1BiJ8we4IghbxVAZM56K4P4IjJDHIBfHH_Uz-p2w9g,609
-dclab/rtdc_dataset/fmt_dcor/tables.py,sha256=rCkKnSoJpQPhjhCgG9hAd6L1wimlIMd7qM5vaNATgbM,1109
+dclab/rtdc_dataset/fmt_dcor/tables.py,sha256=5-RFH8NAQ04LRiOnq0f22FqFirr7lUBkE9_WgxvLzBI,1223
 dclab/rtdc_dataset/fmt_hdf5/__init__.py,sha256=UnitCqiMkY8mMcUKgfLBRVBP5srpTNLrZd3BIRr2tZE,276
 dclab/rtdc_dataset/fmt_hdf5/base.py,sha256=CAcYaN_6X10NK-R1IvlJj6y70lNyAVyT0OnGMs4VMB4,6583
 dclab/rtdc_dataset/fmt_hdf5/basin.py,sha256=qbYgj0RKS9k6RTu5XmYEtgdcbqnVNokD3rAxogyrWrU,822
@@ -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-0.62.9.dist-info/LICENSE,sha256=ayjnuJcdf_kpkDyD61tUcVqVAQaNSYXJ73m5HVB4G8s,18474
-dclab-0.62.9.dist-info/METADATA,sha256=u-w5rYXwQgpAm20yw-JZO8O5NlxpWX8aJRS5U7Vc0_s,4900
-dclab-0.62.9.dist-info/WHEEL,sha256=rTcqimtzpX3smAWAhGmiRSWAxTY4PqYPNE-p4kscHDQ,99
-dclab-0.62.9.dist-info/entry_points.txt,sha256=eOpjgznu-eW-9utUpLU-77O5098YyUEgGF3ksGMdtec,273
-dclab-0.62.9.dist-info/top_level.txt,sha256=irvwZMgs1edY1Zj60ZFk7Almb9Zhk4k6E6aC4YPFnnM,6
-dclab-0.62.9.dist-info/RECORD,,
+dclab-0.62.11.dist-info/LICENSE,sha256=ayjnuJcdf_kpkDyD61tUcVqVAQaNSYXJ73m5HVB4G8s,18474
+dclab-0.62.11.dist-info/METADATA,sha256=yScCpW0rlmyuFdYBYo8cWeP-kL6Y05RCmmo-Sy6ZwS4,4901
+dclab-0.62.11.dist-info/WHEEL,sha256=rTcqimtzpX3smAWAhGmiRSWAxTY4PqYPNE-p4kscHDQ,99
+dclab-0.62.11.dist-info/entry_points.txt,sha256=eOpjgznu-eW-9utUpLU-77O5098YyUEgGF3ksGMdtec,273
+dclab-0.62.11.dist-info/top_level.txt,sha256=irvwZMgs1edY1Zj60ZFk7Almb9Zhk4k6E6aC4YPFnnM,6
+dclab-0.62.11.dist-info/RECORD,,