setup: migrate to dcnum 0.20.0 and fix minor glitch

DC-analysis · May 27, 2024 · 0413333 · 0413333
1 parent edf9926
commit 0413333
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Showing 3 changed files with 15 additions and 6 deletions.
diff --git a/CHANGELOG b/CHANGELOG
@@ -1,3 +1,6 @@
+0.4.0
+ - fix: show correct data PPID in CLI
+ - setup: bump dcnum from 0.19.1 to 0.20.0
 0.3.1
  - ref: migrate from QTableView to QTableWidget (issues with Windows 11)
 0.3.0

diff --git a/chipstream/cli/cli_proc.py b/chipstream/cli/cli_proc.py
@@ -40,7 +40,9 @@ def process_dataset(
     path_out.parent.mkdir(parents=True, exist_ok=True)
 
     # data keyword arguments
-    with dcnum.read.HDF5Data(path_in, pixel_size=pixel_size) as data:
+    data_kwargs = {"pixel_size": pixel_size,
+                   "index_mapping": index_mapping}
+    with dcnum.read.HDF5Data(path_in, **data_kwargs) as data:
         dat_id = data.get_ppid()
     click.echo(f"Data ID:\t{dat_id}")
 
@@ -88,8 +90,7 @@ def process_dataset(
         path_in=path_in,
         path_out=path_out,
         data_code="hdf",
-        data_kwargs={"pixel_size": pixel_size,
-                     "index_mapping": index_mapping},
+        data_kwargs=data_kwargs,
         background_code=bg_cls.get_ppid_code(),
         background_kwargs=bg_kwargs,
         segmenter_code=seg_cls.get_ppid_code(),
@@ -98,7 +99,7 @@ def process_dataset(
         feature_kwargs=feat_kwargs,
         gate_code=gate_cls.get_ppid_code(),
         gate_kwargs=gate_kwargs,
-        no_basins_in_output=True,
+        basin_strategy="drain",
         num_procs=num_cpus,
         debug=debug,
     )

diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -1,5 +1,6 @@
 import dcnum.read
 import h5py
+import numpy as np
 
 import pytest
 
@@ -32,8 +33,12 @@ def test_cli_limit_events(cli_runner, limit_events, dcnum_yield,
 
     # sanity check
     with h5py.File(path) as h5:
-        assert h5["events/frame"][0] == 1
-        assert h5["events/frame"][1] == 2
+        assert np.all(h5["events/frame"][:]
+                      == np.array([1,  2,  2,  4,  4,  5,  5,  5,  6,  6,
+                                   6,  7,  8,  8, 10, 10, 11, 11, 11, 12,
+                                   12, 12, 13, 14, 14, 16, 16, 17, 17, 17,
+                                   18, 18, 18]))
+        assert "basinmap0" not in h5
 
     path_out = path.with_name("limited_events.rtdc")
     result = cli_runner.invoke(cli_main.chipstream_cli,