Changes path length plotter to use measurement vector colour, fixes p…

…ath length saving bug and updates docs

docs/base_computation.rst

@@ -77,9 +77,9 @@ the error for the computation in the dialog shown below.
    :align: center
 
 The error report shows the difference between the measured fiducial points and points estimated using the calculated
-base matrix, and the average norm of the error. The error report could be used to evaluate which points are contributing
-most of error so they could be removed or remeasured, it could reveal situations when the sample is moving (i.e. not
-rigidly mounted), or it could reveal kinematic errors in the robot.
+base matrix, and the distance (euclidean norm) between both sets of points. The error report could be used to evaluate
+which points are contributing most of error so they could be removed or remeasured, it could reveal situations when the
+sample is moving (i.e. not rigidly mounted), or it could reveal kinematic errors in the robot.
 
 Clicking the Accept button in the error report will apply the new base matrix to the positioning system and the change
 in position and orientation can be seen in the graphic window. Clicking the Cancel button will discard the computed

sscanss/app/dialogs/misc.py

@@ -5,7 +5,7 @@
 from PyQt5 import QtCore, QtGui, QtWidgets
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from matplotlib.figure import Figure
-from sscanss.config import path_for, __version__
+from sscanss.config import path_for, __version__, settings
 from sscanss.core.instrument import IKSolver
 from sscanss.core.util import (DockFlag, Attributes, Accordion, Pane, create_tool_button, Banner, compact_path,
                                StyledTabWidget)
@@ -321,7 +321,7 @@ def __init__(self, parent, indices, enabled, points, transform_result, end_confi
         self.banner.hide()
 
         self.main_layout.addSpacing(5)
-        self.result_text = '<p style="font-size:14px">The Average (RMS) Error is ' \
+        self.result_text = '<p style="font-size:14px">The Average Distance Error is ' \
                            '<span style="color:{};font-weight:500;">{:.3f}</span> {}</p>'
         self.result_label = QtWidgets.QLabel()
         self.result_label.setTextFormat(QtCore.Qt.RichText)
@@ -520,13 +520,14 @@ def __init__(self, parent, pose_id, fiducial_id, error):
 
         self.error_table = QtWidgets.QTableWidget()
         self.error_table.setColumnCount(6)
-        self.error_table.setHorizontalHeaderLabels(['Pose ID', 'Fiducial ID', '\u0394X', '\u0394Y', '\u0394Z', 'Norm'])
+        self.error_table.setHorizontalHeaderLabels(['Pose ID', 'Fiducial ID', '\u0394X', '\u0394Y', '\u0394Z',
+                                                    'Euclidean\n Norm'])
         self.error_table.horizontalHeaderItem(0).setToolTip('Index of pose')
         self.error_table.horizontalHeaderItem(1).setToolTip('Index of fiducial point')
         self.error_table.horizontalHeaderItem(2).setToolTip('Difference between computed and measured points (X)')
         self.error_table.horizontalHeaderItem(3).setToolTip('Difference between computed and measured points (Y)')
         self.error_table.horizontalHeaderItem(4).setToolTip('Difference between computed and measured points (Z)')
-        self.error_table.horizontalHeaderItem(5).setToolTip('Magnitude of point differences')
+        self.error_table.horizontalHeaderItem(5).setToolTip('Euclidean distance between and measured points')
 
         self.error_table.setAlternatingRowColors(True)
         self.error_table.setMinimumHeight(600)
@@ -569,7 +570,7 @@ def updateTable(self, pose_id, fiducial_id, error):
         """
         tol = 0.1
         norm = np.linalg.norm(error, axis=1)
-        result_text = '<p style="font-size:14px">The Average (RMS) Error is ' \
+        result_text = '<p style="font-size:14px">The Average Distance Error is ' \
                       '<span style="color:{};font-weight:500;">{:.3f}</span> mm</p>'
         mean = np.mean(norm)
         colour = 'Tomato' if mean > tol else 'SeaGreen'
@@ -761,8 +762,7 @@ def setup(self, no_render=False):
             self.progress_bar.setMaximum(self.simulation.count)
             self.updateProgress(SimulationDialog.State.Starting)
             self.result_list.clear()
-            self.result_counts = {key: 0 for key in self.ResultKey}
-            self.filter_button_group.button(self.ResultKey.Skip.value).setVisible(False)
+            self.resetFilterButtons()
             self.simulation.result_updated.connect(self.showResult)
             self.simulation.stopped.connect(lambda: self.updateProgress(SimulationDialog.State.Stopped))
 
@@ -847,6 +847,13 @@ def getResultKey(self, result):
 
         return key
 
+    def resetFilterButtons(self):
+        self.result_counts = {key: 0 for key in self.ResultKey}
+        for key in self.ResultKey:
+            self.result_counts[key] = 0
+            self.filter_button_group.button(key.value).setText('0')
+        self.filter_button_group.button(self.ResultKey.Skip.value).setVisible(False)
+
     def __updateFilterButton(self, result_key):
         """Updates the filter button for the given key
 
@@ -1225,37 +1232,37 @@ def __init__(self, parent):
         tool_layout.setAlignment(QtCore.Qt.AlignBottom)
         self.main_layout.addLayout(tool_layout)
 
-        layout = QtWidgets.QVBoxLayout()
+        layout = QtWidgets.QHBoxLayout()
         layout.setSpacing(1)
         self.alignment_combobox = QtWidgets.QComboBox()
         self.alignment_combobox.setView(QtWidgets.QListView())
         self.alignment_combobox.addItems(['All', *[f'{i}' for i in range(1, self.simulation.shape[2]+1)]])
         self.alignment_combobox.setMinimumWidth(100)
         self.alignment_combobox.activated.connect(self.plot)
         if self.simulation.shape[2] > 1:
-            layout.addWidget(QtWidgets.QLabel('Alignment'))
+            layout.addWidget(QtWidgets.QLabel('Alignment: '))
             layout.addWidget(self.alignment_combobox)
             tool_layout.addLayout(layout)
 
-        layout = QtWidgets.QVBoxLayout()
+        layout = QtWidgets.QHBoxLayout()
         layout.setSpacing(1)
         self.detector_combobox = QtWidgets.QComboBox()
         self.detector_combobox.setView(QtWidgets.QListView())
         self.detector_combobox.addItems(['Both', *self.simulation.detector_names])
-        self.detector_combobox.setMinimumWidth(50)
+        self.detector_combobox.setMinimumWidth(100)
         self.detector_combobox.activated.connect(self.plot)
         if self.simulation.shape[1] > 1:
-            layout.addWidget(QtWidgets.QLabel('Detector'))
+            layout.addWidget(QtWidgets.QLabel('Detector: '))
             layout.addWidget(self.detector_combobox)
             tool_layout.addLayout(layout)
 
-        layout = QtWidgets.QVBoxLayout()
-        layout.setSpacing(1)
+        # layout = QtWidgets.QVBoxLayout()
+        # layout.setSpacing(1)
         self.grid_checkbox = QtWidgets.QCheckBox('Show Grid')
         self.grid_checkbox.clicked.connect(self.plot)
-        layout.addSpacing(15)
-        layout.addWidget(self.grid_checkbox)
-        tool_layout.addLayout(layout)
+        # layout.addSpacing(15)
+        tool_layout.addWidget(self.grid_checkbox)
+        # tool_layout.addLayout(layout)
 
         tool_layout.addStretch(1)
         self.export_button = QtWidgets.QPushButton('Export')
@@ -1288,17 +1295,14 @@ def export(self):
             if os.path.splitext(filename)[1].lower() == '.txt':
                 header = 'Index'
                 data = [self.axes.lines[0].get_xdata()]
+                fmt = ['%d']
                 for line in self.axes.lines:
                     data.append(line.get_ydata())
+                    fmt.append('%.3f')
                     header = f'{header}\t{line.get_label()}'
 
-                alignment = self.alignment_combobox.currentIndex()
-                if alignment == 0:
-                    header = f'Path lengths for each measurement\n{header}'
-                else:
-                    header = f'Path lengths for each measurement in vector alignment {alignment}\n{header}'
-                np.savetxt(filename, np.column_stack(data), fmt=['%d', '%.3f', '%.3f'], delimiter='\t',
-                           header=header, comments='')
+                header = f'{self.axes.get_title()}\n{header}'
+                np.savetxt(filename, np.column_stack(data), fmt=fmt, delimiter='\t', header=header, comments='')
             else:
                 self.figure.savefig(filename, dpi=300, bbox_inches='tight')
         except OSError as e:
@@ -1314,26 +1318,32 @@ def plot(self):
 
         names = self.simulation.detector_names
         path_length = self.simulation.path_lengths
+        colours = [None] * len(names)
+        colours[:2] = [settings.value(settings.Key.Vector_1_Colour), settings.value(settings.Key.Vector_2_Colour)]
         if detector_index > -1:
             names = names[detector_index:detector_index+1]
             path_length = path_length[:, detector_index:detector_index+1, :]
+            colours = colours[detector_index:detector_index+1]
 
         if alignment_index > -1:
             path_length = path_length[:, :, alignment_index]
+            title = f'Path lengths for measurements in alignment {alignment_index + 1}'
         else:
             if self.simulation.args['align_first_order']:
                 path_length = np.column_stack(np.dsplit(path_length, path_length.shape[2])).reshape(-1, len(names))
             else:
                 path_length = np.row_stack(np.dsplit(path_length, path_length.shape[2])).reshape(-1, len(names))
+            title = 'Path lengths for measurements'
 
         label = np.arange(1, path_length.shape[0] + 1)
         step = 1 if path_length.shape[0] < 10 else path_length.shape[0] // 10
 
         self.axes.set_xticks(label[::step])
         for i in range(path_length.shape[1]):
-            self.axes.plot(label, path_length[:, i], 'o-', label=names[i])
+            self.axes.plot(label, path_length[:, i], 'o-', label=names[i], color=colours[i])
 
         self.axes.legend()
+        self.axes.set_title(title)
         self.axes.set_xlabel('Measurement Index', labelpad=10)
         self.axes.set_ylabel('Path Length (mm)')
         self.axes.minorticks_on()

tests/test_widgets.py

@@ -1238,13 +1238,15 @@ def testExport(self, savetxt):
         expected = [[1, 1, 2], [2, 0, 0], [3, 3, 4], [4, 0, 0], [5, 5, 6], [6, 0, 0]]
         self.assertEqual(savetxt.call_count, 2)
         np.testing.assert_array_almost_equal(savetxt.call_args[0][1], expected, decimal=5)
+        self.assertEqual(len(savetxt.call_args[1]['fmt']), 3)
 
         combo = self.dialog.alignment_combobox
         combo.setCurrentIndex(2)
         combo.activated.emit(2)
         self.dialog.export()
         self.assertEqual(savetxt.call_count, 3)
         np.testing.assert_array_almost_equal(savetxt.call_args[0][1], [[1, 0, 0], [2, 0, 0], [3, 0, 0]], decimal=5)
+        self.assertEqual(len(savetxt.call_args[1]['fmt']), 3)
 
         combo.setCurrentIndex(1)
         combo = self.dialog.detector_combobox
@@ -1253,6 +1255,7 @@ def testExport(self, savetxt):
         self.dialog.export()
         self.assertEqual(savetxt.call_count, 4)
         np.testing.assert_array_almost_equal(savetxt.call_args[0][1], [[1, 2], [2, 4], [3, 6]], decimal=5)
+        self.assertEqual(len(savetxt.call_args[1]['fmt']), 2)
 
         self.presenter.notifyError.assert_not_called()
         savetxt.side_effect = OSError