fix: ValueError when trying to compute contour spacing; coloring scatter plot by feature did not work; search path in session should not be filename

Author: paulmueller

CHANGELOG

@@ -1,3 +1,10 @@
+2.1.2
+ - fix: ValueError when trying to compute contour spacing, because no
+   datasets are selected for a plot
+ - fix: coloring scatter plot by feature did not work when the feature
+   contains nan values
+ - fix: search path in session should not be filename but its
+   directory
 2.1.1
  - fix: include private datasets when searching with DCOR API Key
  - fix: remove UI option to compute Young's modulus for reservoir data

shapeout2/gui/analysis/ana_plot.py

@@ -337,31 +337,32 @@ def _set_contour_spacing_auto(self, axis_x=None, axis_y=None):
             return
         else:
             self.setEnabled(True)
-        spacings_xy = []
-        for axis, scaleCombo in zip([axis_x, axis_y],
-                                    [self.comboBox_scale_x,
-                                     self.comboBox_scale_y]):
-            if axis is None:
-                # nothing to do
-                spacings_xy.append(None)
-            else:
-                # determine good approximation
-                dslist, _ = self.pipeline.get_plot_datasets(
-                    self.current_plot.identifier)
-                spacings = []
-                for ds in dslist:
-                    spa = ds.get_kde_spacing(
-                        a=ds[axis],
-                        feat=axis,
-                        scale=scaleCombo.currentData(),
-                        method=dclab.kde_methods.bin_width_percentile,
-                    )
-                    spacings.append(spa)
-                spacings_xy.append(np.min(spacings))
-        spacing_x, spacing_y = spacings_xy
-        # sets the limits before setting the value
-        self._set_contour_spacing(spacing_x=spacing_x,
-                                  spacing_y=spacing_y)
+        dslist, _ = self.pipeline.get_plot_datasets(
+            self.current_plot.identifier)
+        if dslist:
+            spacings_xy = []
+            for axis, scaleCombo in zip([axis_x, axis_y],
+                                        [self.comboBox_scale_x,
+                                         self.comboBox_scale_y]):
+                if axis is None:
+                    # nothing to do
+                    spacings_xy.append(None)
+                else:
+                    # determine good approximation
+                    spacings = []
+                    for ds in dslist:
+                        spa = ds.get_kde_spacing(
+                            a=ds[axis],
+                            feat=axis,
+                            scale=scaleCombo.currentData(),
+                            method=dclab.kde_methods.bin_width_percentile,
+                        )
+                        spacings.append(spa)
+                    spacings_xy.append(np.min(spacings))
+            spacing_x, spacing_y = spacings_xy
+            # sets the limits before setting the value
+            self._set_contour_spacing(spacing_x=spacing_x,
+                                      spacing_y=spacing_y)
 
     @property
     def current_plot(self):

shapeout2/gui/main.py

@@ -550,12 +550,13 @@ def on_action_import_filter(self):
             # update UI
             self.reload_pipeline()
 
-    def on_action_open(self):
+    def on_action_open(self, path=None):
         if self.pipeline.slots or self.pipeline.filters:
             if not self.on_action_clear():
                 return
-        path, _ = QtWidgets.QFileDialog.getOpenFileName(
-            self, 'Open session', '', 'Shape-Out 2 session (*.so2)')
+        if path is None:
+            path, _ = QtWidgets.QFileDialog.getOpenFileName(
+                self, 'Open session', '', 'Shape-Out 2 session (*.so2)')
         if path:
             search_paths = []
             while True:

shapeout2/gui/pipeline_plot.py

@@ -478,7 +478,10 @@ def add_scatter(plot_item, plot_state, rtdc_ds, slot_state):
         feat -= sca["hue min"]
         feat /= sca["hue max"] - sca["hue min"]
         for f in feat:
-            brush.append(cmap.mapToQColor(f))
+            if np.isnan(f):
+                brush.append(pg.mkColor("#FF0000"))
+            else:
+                brush.append(cmap.mapToQColor(f))
     elif sca["marker hue"] == "dataset":
         alpha = int(sca["marker alpha"] * 255)
         colord = pg.mkColor(slot_state["color"])

shapeout2/session.py

@@ -192,7 +192,7 @@ def save_session(path, pipeline):
         if slot.format == "hdf5":
             # search path
             try:
-                rel = os.path.relpath(slot.path, path.parent)
+                rel = os.path.relpath(slot.path.parent, path.parent)
             except (OSError, ValueError):
                 rel = "."
             search_paths[slot.identifier] = rel

tests/test_gui_plotting.py

@@ -8,6 +8,9 @@
 from shapeout2 import pipeline, session
 
 
+datapath = pathlib.Path(__file__).parent / "data"
+
+
 @pytest.fixture(autouse=True)
 def run_around_tests():
     # Code that will run before your test, for example:
@@ -18,6 +21,45 @@ def run_around_tests():
     session.clear_session()
 
 
+def test_handle_axis_selection_empty_plot(qtbot):
+    """User did not add a dataset to a plot and starts changing plot params"""
+    mw = ShapeOut2()
+    qtbot.addWidget(mw)
+
+    # add a dataslot
+    path = datapath / "calibration_beads_47.rtdc"
+    mw.add_dataslot(paths=[path])
+
+    # add a plot
+    plot_id = mw.add_plot()
+
+    assert len(mw.pipeline.slot_ids) == 1, "we added that"
+    assert len(mw.pipeline.filter_ids) == 1, "automatically added"
+    assert len(mw.pipeline.plot_ids) == 1, "we added that"
+
+    # activate analysis view
+    pe = mw.block_matrix.get_widget(filt_plot_id=plot_id)
+    qtbot.mouseClick(pe.toolButton_modify, QtCore.Qt.LeftButton)
+
+    pv = mw.widget_ana_view.widget_plot
+
+    # This lead to:
+    #    Traceback (most recent call last):
+    #  File "/ShapeOut2/shapeout2/gui/analysis/ana_plot.py",
+    #     line 406, in on_axis_changed
+    #    self._set_contour_spacing_auto(axis_y=gen["axis y"])
+    #  File "/ShapeOut2/shapeout2/gui/analysis/ana_plot.py",
+    #     line 361, in _set_contour_spacing_auto
+    #    spacings_xy.append(np.min(spacings))
+    #  File "/numpy/core/fromnumeric.py", line 2618, in amin
+    #    initial=initial)
+    #  File "/numpy/core/fromnumeric.py", line 86, in _wrapreduction
+    #    return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
+    # ValueError: zero-size array to reduction operation minimum which
+    # has no identity
+    pv.comboBox_axis_y.setCurrentIndex(pv.comboBox_axis_y.findData("emodulus"))
+
+
 def test_handle_empty_plots_issue_27(qtbot):
     """Correctly handle empty plots
 
@@ -27,7 +69,7 @@ def test_handle_empty_plots_issue_27(qtbot):
     qtbot.addWidget(mw)
 
     # add a dataslot
-    path = pathlib.Path(__file__).parent / "data" / "calibration_beads_47.rtdc"
+    path = datapath / "calibration_beads_47.rtdc"
     mw.add_dataslot(paths=[path])
     # add another one
     mw.add_dataslot(paths=[path])
@@ -70,6 +112,19 @@ def test_handle_empty_plots_issue_27(qtbot):
         qtbot.mouseClick(pe, QtCore.Qt.LeftButton)  # activate (raises #27)
 
 
+def test_handle_nan_valued_feature_color(qtbot):
+    """User wants to color scatter data points with feature containing nans"""
+    spath = datapath / "version_2_1_2_plot_color_emodulus.so2"
+
+    mw = ShapeOut2()
+    qtbot.addWidget(mw)
+
+    # lead to:
+    # OverflowError: argument 4 overflowed: value must be in the range
+    # -2147483648 to 2147483647
+    mw.on_action_open(spath)
+
+
 def test_remove_plots_issue_36(qtbot):
     """Correctly handle empty plots
 
@@ -85,7 +140,7 @@ def test_remove_plots_issue_36(qtbot):
     qtbot.addWidget(mw)
 
     # add a dataslots
-    path = pathlib.Path(__file__).parent / "data" / "calibration_beads_47.rtdc"
+    path = datapath / "calibration_beads_47.rtdc"
     mw.add_dataslot(paths=[path, path, path])
 
     assert len(mw.pipeline.slot_ids) == 3, "we added those"