tests: add test for bulk emodulus computation (#60)

Author: paulmueller

shapeout2/gui/bulk/bulk_emodulus.py

@@ -85,9 +85,9 @@ def set_emodulus_properties(self):
         """Set the given emodulus properties for all datasets"""
         medium = self.comboBox_medium.currentData()
         if self.comboBox_temp.isEnabled():
-            temp = self.comboBox_temp.currentData()
+            scen = self.comboBox_temp.currentData()
         else:
-            temp = None
+            scen = None
         if self.doubleSpinBox_temp.isEnabled():
             tempval = self.doubleSpinBox_temp.value()
         else:
@@ -105,27 +105,24 @@ def set_emodulus_properties(self):
 
             # Use the internal sanity checks to determine whether
             # or not we can set the medium or temperature scenarios.
-            choices_medium = SlotPanel.get_dataset_choices_medium(ds)
-            choices_temp = SlotPanel.get_dataset_choices_temperature(ds)
-            if medium in [m[1] for m in choices_medium]:
+            valid_media = SlotPanel.get_dataset_choices_medium(ds)
+            valid_scenarios = SlotPanel.get_dataset_choices_temperature(ds)
+            if medium in [m[1] for m in valid_media]:
                 state = slot.__getstate__()
                 state["emodulus"]["emodulus medium"] = medium
-                slot.__setstate__(state)
-
                 # Set the viscosity here, because unknown media are
                 # available.
                 if viscval is not None:
                     state["emodulus"]["emodulus viscosity"] = viscval
+                slot.__setstate__(state)
 
-            if temp in [t[1] for t in choices_temp]:  # temp is not None
+            if scen in [s[1] for s in valid_scenarios]:  # scen is not None
                 state = slot.__getstate__()
-                state["emodulus"]["emodulus scenario"] = temp
+                state["emodulus"]["emodulus scenario"] = scen
                 if tempval is not None:
                     state["emodulus"]["emodulus temperature"] = tempval
                 slot.__setstate__(state)
 
-            print(state["emodulus"])
-
     def update_ui(self):
         """Update all relevant parts of the main user interface"""
         state = self.pipeline.__getstate__()

tests/conftest.py

@@ -1,6 +1,14 @@
+import shutil
+import tempfile
+import time
+
 from PyQt5 import QtCore
 
 
+TMPDIR = tempfile.mkdtemp(prefix=time.strftime(
+    "shapeout2_test_%H.%M_"))
+
+
 def pytest_configure(config):
     """This is ran before all tests"""
     # disable update checking
@@ -13,3 +21,13 @@ def pytest_configure(config):
     settings.setValue("check for updates", 0)
     settings.setValue("advanced/check pyqtgraph version", 0)
     settings.sync()
+    # set global temp directory
+    tempfile.tempdir = TMPDIR
+
+
+def pytest_unconfigure(config):
+    """
+    called before test process is exited.
+    """
+    # clear global temp directory
+    shutil.rmtree(TMPDIR, ignore_errors=True)

tests/test_gui_bulk_emodulus.py

@@ -0,0 +1,180 @@
+"""Test bulk action for emodulus computation"""
+import pathlib
+import tempfile
+
+import dclab
+import h5py
+import numpy as np
+import pytest
+
+from shapeout2.gui.main import ShapeOut2
+from shapeout2.gui import bulk
+from shapeout2 import session
+
+
+datapath = pathlib.Path(__file__).parent / "data"
+
+
+def make_dataset(medium="CellCarrier", temp=22.5, temp_range=[22, 23],
+                 chip_region="channel"):
+    # create a fake dataset
+    path = datapath / "calibration_beads_47.rtdc"
+    ds = dclab.new_dataset(path)
+    tmp = tempfile.mktemp(".rtdc", prefix="example_")
+    ds.export.hdf5(tmp, features=["deform", "area_um", "bright_avg"])
+    with h5py.File(tmp, mode="a") as h5:
+        h5["events/temp"] = np.linspace(temp_range[0], temp_range[1], len(ds))
+        if medium is None:
+            h5.attrs.pop("setup:medium")
+        else:
+            h5.attrs["setup:medium"] = medium
+        h5.attrs["setup:temperature"] = temp
+        h5.attrs["setup:chip region"] = chip_region
+    return pathlib.Path(tmp)
+
+
+@pytest.fixture(autouse=True)
+def run_around_tests():
+    # Code that will run before your test, for example:
+    session.clear_session()
+    # A test function will be run at this point
+    yield
+    # Code that will run after your test, for example:
+    session.clear_session()
+
+
+def test_manual_basic(qtbot):
+    """Most simple test"""
+    mw = ShapeOut2()
+    qtbot.addWidget(mw)
+
+    # add a dataslot
+    path = datapath / "calibration_beads_47.rtdc"
+    mw.add_dataslot(paths=[path])
+    mw.add_dataslot(paths=[path])
+
+    # sanity check (no emodulus should be available)
+    for slot in mw.pipeline.slots:
+        ds = slot.get_dataset()
+        assert "emodulus" not in ds
+        assert ds.config["setup"]["medium"] == "CellCarrierB"
+
+    # create bulk action dialog manually
+    dlg = bulk.BulkActionEmodulus(mw, pipeline=mw.pipeline)
+    dlg.comboBox_temp.setCurrentIndex(dlg.comboBox_temp.findData("manual"))
+    dlg.doubleSpinBox_temp.setValue(29.5)
+    dlg.on_ok()
+
+    for slot in mw.pipeline.slots:
+        ds = slot.get_dataset()
+        assert "emodulus" in ds
+        assert ds.config["setup"]["medium"] == "CellCarrierB"
+        assert ds.config["calculation"]["emodulus model"] == "elastic sphere"
+        assert ds.config["calculation"]["emodulus medium"] == "CellCarrierB"
+        assert ds.config["calculation"]["emodulus temperature"] == 29.5
+        assert "emodulus viscosity" not in ds.config["calculation"]
+
+
+def test_manual_wrong_medium(qtbot):
+    """Deliberately set wrong medium"""
+    mw = ShapeOut2()
+    qtbot.addWidget(mw)
+
+    # add a dataslot
+    path = datapath / "calibration_beads_47.rtdc"
+    mw.add_dataslot(paths=[path])
+    mw.add_dataslot(paths=[path])
+
+    # create bulk action dialog manually
+    dlg = bulk.BulkActionEmodulus(mw, pipeline=mw.pipeline)
+    dlg.comboBox_temp.setCurrentIndex(dlg.comboBox_temp.findData("manual"))
+    dlg.doubleSpinBox_temp.setValue(29.5)
+    # Set medium to "water". This should not change the emodulus medium.
+    dlg.comboBox_medium.setCurrentIndex(dlg.comboBox_medium.findData("water"))
+
+    dlg.on_ok()
+
+    for slot in mw.pipeline.slots:
+        ds = slot.get_dataset()
+        assert "emodulus" in ds
+        assert ds.config["setup"]["medium"] == "CellCarrierB"
+        assert ds.config["calculation"]["emodulus model"] == "elastic sphere"
+        assert ds.config["calculation"]["emodulus medium"] == "CellCarrierB"
+        assert ds.config["calculation"]["emodulus temperature"] == 29.5
+        assert "emodulus viscosity" not in ds.config["calculation"]
+
+
+def test_temperature_feature(qtbot):
+    mw = ShapeOut2()
+    qtbot.addWidget(mw)
+
+    # add custom dataslot
+    path = make_dataset(medium="CellCarrier", temp=22.5, temp_range=[22, 23])
+    mw.add_dataslot(paths=[path])
+    mw.add_dataslot(paths=[path])
+
+    # create bulk action dialog manually
+    dlg = bulk.BulkActionEmodulus(mw, pipeline=mw.pipeline)
+    dlg.comboBox_temp.setCurrentIndex(dlg.comboBox_temp.findData("feature"))
+    dlg.on_ok()
+
+    for slot in mw.pipeline.slots:
+        ds = slot.get_dataset()
+        assert "emodulus" in ds
+        assert ds.config["setup"]["medium"] == "CellCarrier"
+        assert ds.config["calculation"]["emodulus model"] == "elastic sphere"
+        assert ds.config["calculation"]["emodulus medium"] == "CellCarrier"
+        assert "emodulus temperature" not in ds.config["calculation"]
+        assert "emodulus viscosity" not in ds.config["calculation"]
+
+
+def test_viscosity(qtbot):
+    mw = ShapeOut2()
+    qtbot.addWidget(mw)
+
+    # add custom dataslot
+    path = make_dataset(medium="other")
+    mw.add_dataslot(paths=[path])
+    mw.add_dataslot(paths=[path])
+
+    # create bulk action dialog manually
+    dlg = bulk.BulkActionEmodulus(mw, pipeline=mw.pipeline)
+    dlg.comboBox_medium.setCurrentIndex(dlg.comboBox_medium.findData("other"))
+    dlg.doubleSpinBox_visc.setValue(1.0)
+    dlg.on_ok()
+
+    for slot in mw.pipeline.slots:
+        ds = slot.get_dataset()
+        assert "emodulus" in ds
+        assert ds.config["setup"]["medium"] == "other"
+        assert ds.config["calculation"]["emodulus model"] == "elastic sphere"
+        assert "emodulus medium" not in ds.config["calculation"]
+        assert "emodulus temperature" not in ds.config["calculation"]
+        assert ds.config["calculation"]["emodulus viscosity"] == 1.0
+
+
+def test_wrong_medium_viscosity(qtbot):
+    """Deliberately set wrong visosity"""
+    mw = ShapeOut2()
+    qtbot.addWidget(mw)
+
+    # add a dataslot
+    path = datapath / "calibration_beads_47.rtdc"
+    mw.add_dataslot(paths=[path])
+    mw.add_dataslot(paths=[path])
+
+    # create bulk action dialog manually
+    dlg = bulk.BulkActionEmodulus(mw, pipeline=mw.pipeline)
+    dlg.comboBox_medium.setCurrentIndex(dlg.comboBox_medium.findData("other"))
+    dlg.doubleSpinBox_visc.setValue(1.0)  # random number
+
+    dlg.on_ok()
+
+    for slot in mw.pipeline.slots:
+        ds = slot.get_dataset()
+        assert "emodulus" not in ds, "because medium is fixed"
+        assert ds.config["setup"]["medium"] == "CellCarrierB"
+        assert ds.config["calculation"]["emodulus model"] == "elastic sphere"
+        assert ds.config["calculation"]["emodulus medium"] == "CellCarrierB"
+        assert "emodulus temperature" not in ds.config["calculation"]
+        assert "emodulus viscosity" not in ds.config["calculation"]