Merge pull request #54 from GuckLab/fix/53/bump-bmlab

fix: bump bmlab from 0.2.3 to 0.6.1 (file format changes) (close #53)

CHANGELOG

@@ -1,3 +1,5 @@
+0.4.0
+ - fix: bump bmlab from 0.2.3 to 0.6.1 (file format changes) (#53)
 0.3.1
  - fix: bump bmlab from 0.1.10 to 0.2.3 (file format changes) (#49)
 0.3.0

setup.py

@@ -28,7 +28,7 @@
     description=description,
     long_description=open('README.rst').read() if exists('README.rst') else '',
     install_requires=["czifile==2019.7.2",  # bc cgohlke and used for signature
-                      "bmlab==0.5.1",
+                      "bmlab==0.6.1",
                       "h5py>=2.10.0",
                       "numpy>=1.17.0",
                       "pyqt6>=6.2.0",

tests/test_fmt_h5_brillouin_bmlab.py

@@ -6,48 +6,51 @@
 
 
 def test_load_bmlab_brillouin():
-    paths = retrieve_data("fmt_brillouin-h5_bmlab-session_2022.zip")
+    paths = retrieve_data("fmt_brillouin-h5_bmlab-session_2022_water.zip")
     data, meta = formats.load(paths[0])
 
     # check metadata
     assert meta["pixel size x"] == 1
     assert meta["pixel size y"] == 1
     assert np.isnan(meta["pixel size z"])
     assert meta["shape"] == (3, 5, 1)
-    assert "brillouin_peak_position" in meta["channel hues"]
+    assert "brillouin_peak_position_f" in meta["channel hues"]
 
     # check data
-    assert "brillouin_peak_position" in data
-    assert data["brillouin_peak_position"].shape == (3, 5, 1)
-    assert data["brillouin_peak_position"][2, 3, 0] == 62.28071301762982
-    assert meta["signature"] == "25d6ae8774fc29417facc6c9dfe061e6"
+    assert "brillouin_peak_position_f" in data
+    assert data["brillouin_peak_position_f"].shape == (3, 5, 1)
+    assert data["brillouin_peak_position_f"][2, 3, 0] == 7.418597699375756
+    assert meta["signature"] == "7692028641e09f26ad0c8caf010ecaeb"
 
 
 def test_load_bmlab_brillouin_2rep():
-    paths = retrieve_data("fmt_brillouin-h5_bmlab-session_2022_2-rep.zip")
+    paths =\
+        retrieve_data("fmt_brillouin-h5_bmlab-session_2022_water_2-rep.zip")
     data, meta = formats.load(paths[0])
 
     # check metadata
     assert meta["pixel size x"] == 1
     assert meta["pixel size y"] == 1
     assert np.isnan(meta["pixel size z"])
     assert meta["shape"] == (3, 5, 1)
-    assert "rep-0_brillouin_peak_position" in meta["channel hues"]
-    assert "rep-1_brillouin_peak_position" in meta["channel hues"]
+    assert "rep-0_brillouin_peak_position_f" in meta["channel hues"]
+    assert "rep-1_brillouin_peak_position_f" in meta["channel hues"]
 
     # check data
-    assert "rep-0_brillouin_peak_position" in data
-    assert data["rep-0_brillouin_peak_position"].shape == (3, 5, 1)
-    assert data["rep-0_brillouin_peak_position"][2, 3, 0] == 55.53730853499501
-    assert "rep-1_brillouin_peak_position" in data
-    assert data["rep-1_brillouin_peak_position"].shape == (3, 5, 1)
-    assert data["rep-1_brillouin_peak_position"][2, 3, 0] == 101.47705516241298
+    assert "rep-0_brillouin_peak_position_f" in data
+    assert data["rep-0_brillouin_peak_position_f"].shape == (3, 5, 1)
+    assert data["rep-0_brillouin_peak_position_f"][2, 3, 0] ==\
+           7.414767296701641
+    assert "rep-1_brillouin_peak_position_f" in data
+    assert data["rep-1_brillouin_peak_position_f"].shape == (3, 5, 1)
+    assert data["rep-1_brillouin_peak_position_f"][2, 3, 0] ==\
+           7.4293433545770124
 
-    assert meta["signature"] == "0f9dfe4cfe549859ac09ec0ead5bf58f"
+    assert meta["signature"] == "0fa3675745a06d6c54184aa95873280e"
 
 
 def test_load_bmlab_brillouin_signature():
-    paths = retrieve_data("fmt_brillouin-h5_bmlab-session_2022.zip")
+    paths = retrieve_data("fmt_brillouin-h5_bmlab-session_2022_water.zip")
     _, meta1 = formats.load(paths[0])
     _, meta2 = formats.load(paths[1])
     assert meta1["signature"] == meta2["signature"]

tests/test_gui_collect.py

@@ -17,6 +17,30 @@ def test_basic(qtbot):
     mw.close()
 
 
+def test_load_bmlab_brillouin_data(qtbot, monkeypatch):
+    paths = retrieve_data("fmt_brillouin-h5_bmlab-session_2022_water.zip")
+
+    mw = Impose()
+    qtbot.addWidget(mw)
+    monkeypatch.setattr(QtWidgets.QFileDialog, "getOpenFileNames",
+                        lambda *args: ([str(paths[0])], None))
+    qtbot.mouseClick(mw.tab_collect.toolButton_add_data,
+                     QtCore.Qt.MouseButton.LeftButton)
+    QtWidgets.QApplication.processEvents(
+        QtCore.QEventLoop.ProcessEventsFlag.AllEvents, 300)
+
+    # select the first entry in the datasets list (actual data)
+    qtbot.mouseClick(mw.tab_collect.tableWidget_paths.cellWidget(0, 0),
+                     QtCore.Qt.MouseButton.LeftButton)
+    # sanity check (no data displayed)
+    assert mw.tab_collect.groupBox_struct.isEnabled()
+
+    # select the second entry in the visualization list
+    item = mw.tab_collect.vis.listWidget_chan.item(1)
+    item.setCheckState(QtCore.Qt.CheckState.Checked)
+    assert mw.tab_collect.groupBox_struct.isEnabled()
+
+
 def test_load_bmlab_brillouin_with_nan_data(qtbot, monkeypatch):
     paths = retrieve_data("fmt_brillouin-h5_bmlab-session_2022.zip")
 
@@ -36,10 +60,9 @@ def test_load_bmlab_brillouin_with_nan_data(qtbot, monkeypatch):
     assert not mw.tab_collect.groupBox_struct.isEnabled()
 
     # select the second entry in the visualization list
-    # (the first entry contains nans, the second entry contains data)
     item = mw.tab_collect.vis.listWidget_chan.item(1)
     item.setCheckState(QtCore.Qt.CheckState.Checked)
-    assert mw.tab_collect.groupBox_struct.isEnabled()
+    assert not mw.tab_collect.groupBox_struct.isEnabled()
 
 
 def test_load_dataset(qtbot, monkeypatch):