invert the image array, show user comments in the GUI

mesmerize/viewer/modules/femtonics_mesc.py

@@ -13,6 +13,21 @@
 from re import sub as regex_sub
 from ...pyqtgraphCore import PlotWidget
 import numpy as np
+from cv2 import bitwise_not
+
+
+def ascii_to_str(array: np.ndarray):
+    """
+    Get a string from an array of ascii integers
+
+    :param array: array of integers representing ascii chars
+    :return: string represented by the array
+    """
+    return ''.join(
+        map(
+            chr, filter(None, array)
+        )
+    )
 
 
 # Navigator object which helps control the
@@ -248,6 +263,7 @@ def __init__(self, parent, viewer_ref):  # when a ModuleGUI() is instantiated th
         ]
 
         self.mesc_navigator = MEScNavigator(self, list_widgets)
+        self.mesc_navigator.sig_hpath_changed.connect(self.set_comment_line)
         self.mesc_navigator.sig_hpath_changed.connect(self._enable_import_button)
 
         self.mesc_navigator.sig_channel_doubleclicked.connect(
@@ -322,6 +338,16 @@ def _channel_doubleclicked(self, hpath: dict):
 
             self.plot_widgets.append(pw)
 
+    def set_comment_line(self, hpath: dict):
+        if hpath['unit']:
+            f = self.mesc_navigator.file
+            comment = f[hpath['session']][hpath['unit']].attrs['Comment']
+            comment = ascii_to_str(comment)
+            self.ui.lineEdit_comment.setText(comment)
+
+        else:
+            self.ui.lineEdit_comment.clear()
+
     @present_exceptions(
         'Could not import recording',
         'The following error occurred while trying to import the chosen recording'
@@ -339,7 +365,9 @@ def import_recording(self, *args):
         # Load the image sequence stored in this `MUnit_X`
         f = self.mesc_navigator.file  # hdf file handle
         hpath = self.mesc_navigator.get_hpath(str)  # hdf path
-        img_seq = f[hpath][()]  # image array
+        img_seq = bitwise_not(  # load & invert image array
+            f[hpath][()]
+        )
 
         sess = self.mesc_navigator.get_hpath(dict)['session']
         unit = self.mesc_navigator.get_hpath(dict)['unit']
@@ -348,6 +376,10 @@ def import_recording(self, *args):
             f[sess][unit].attrs['ZAxisConversionConversionLinearScale'] + \
             f[sess][unit].attrs['ZAxisConversionConversionLinearOffset']
 
+        z_units = ascii_to_str(f[sess][unit].attrs['ZAxisConversionUnitName'])
+        if z_units != 'ms':
+            raise TypeError(f"Z-axis units <{z_units}> not supported")
+
         # get the sampling rate
         fps = 1 / (frame_time / 1000)  # for now just assuming the frame time are always in milliseconds
 
@@ -376,3 +408,6 @@ def import_recording(self, *args):
 
         # Update the GUI according to the new ViewerWorkEnv
         self.vi.update_workEnv()
+
+        # set the "Current Image sequence" in the Viewer
+        self.vi.viewer.ui.label_curr_img_seq_name.setText(hpath)

mesmerize/viewer/modules/pytemplates/femtonics_mesc_template.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-# Form implementation generated from reading ui file './ui_files/femtonics_mesc_template.ui'
+# Form implementation generated from reading ui file './femtonics_mesc_template.ui'
 #
 # Created by: PyQt5 UI code generator 5.9.2
 #
@@ -85,6 +85,16 @@ def setupUi(self, DockWidget):
         self.verticalLayout_3.addWidget(self.listWidget_channel)
         self.horizontalLayout_2.addLayout(self.verticalLayout_3)
         self.verticalLayout_5.addLayout(self.horizontalLayout_2)
+        self.horizontalLayout_5 = QtWidgets.QHBoxLayout()
+        self.horizontalLayout_5.setObjectName("horizontalLayout_5")
+        self.label_5 = QtWidgets.QLabel(self.tab_mesc_file)
+        self.label_5.setObjectName("label_5")
+        self.horizontalLayout_5.addWidget(self.label_5)
+        self.lineEdit_comment = QtWidgets.QLineEdit(self.tab_mesc_file)
+        self.lineEdit_comment.setReadOnly(True)
+        self.lineEdit_comment.setObjectName("lineEdit_comment")
+        self.horizontalLayout_5.addWidget(self.lineEdit_comment)
+        self.verticalLayout_5.addLayout(self.horizontalLayout_5)
         self.label_4 = QtWidgets.QLabel(self.tab_mesc_file)
         font = QtGui.QFont()
         font.setPointSize(14)
@@ -119,7 +129,8 @@ def setupUi(self, DockWidget):
         DockWidget.setTabOrder(self.pushButton_close_file, self.listWidget_session)
         DockWidget.setTabOrder(self.listWidget_session, self.listWidget_unit)
         DockWidget.setTabOrder(self.listWidget_unit, self.listWidget_channel)
-        DockWidget.setTabOrder(self.listWidget_channel, self.pushButton_import_image)
+        DockWidget.setTabOrder(self.listWidget_channel, self.lineEdit_comment)
+        DockWidget.setTabOrder(self.lineEdit_comment, self.pushButton_import_image)
         DockWidget.setTabOrder(self.pushButton_import_image, self.pushButton_import_stim_map)
 
     def retranslateUi(self, DockWidget):
@@ -131,6 +142,8 @@ def retranslateUi(self, DockWidget):
         self.label.setText(_translate("DockWidget", "Session"))
         self.label_2.setText(_translate("DockWidget", "Unit"))
         self.label_3.setText(_translate("DockWidget", "Channel"))
+        self.label_5.setText(_translate("DockWidget", "Comment:"))
+        self.lineEdit_comment.setToolTip(_translate("DockWidget", "Comment stored in the selected MUnit"))
         self.label_4.setText(_translate("DockWidget", "Import:"))
         self.pushButton_import_image.setText(_translate("DockWidget", "Image"))
         self.pushButton_import_stim_map.setText(_translate("DockWidget", "Stim Map"))

mesmerize/viewer/modules/ui_files/femtonics_mesc_template.ui

@@ -150,6 +150,27 @@
           </item>
          </layout>
         </item>
+        <item>
+         <layout class="QHBoxLayout" name="horizontalLayout_5">
+          <item>
+           <widget class="QLabel" name="label_5">
+            <property name="text">
+             <string>Comment:</string>
+            </property>
+           </widget>
+          </item>
+          <item>
+           <widget class="QLineEdit" name="lineEdit_comment">
+            <property name="toolTip">
+             <string>Comment stored in the selected MUnit</string>
+            </property>
+            <property name="readOnly">
+             <bool>true</bool>
+            </property>
+           </widget>
+          </item>
+         </layout>
+        </item>
         <item>
          <widget class="QLabel" name="label_4">
           <property name="font">
@@ -221,6 +242,7 @@
   <tabstop>listWidget_session</tabstop>
   <tabstop>listWidget_unit</tabstop>
   <tabstop>listWidget_channel</tabstop>
+  <tabstop>lineEdit_comment</tabstop>
   <tabstop>pushButton_import_image</tabstop>
   <tabstop>pushButton_import_stim_map</tabstop>
  </tabstops>