Merge pull request #522 from open-ephys/issue-366-v2

Move Neuropixels V1 ProbeInterface configurations from Bonsai file to JSON files

Author: bparks13

OpenEphys.Onix1.Design/ChannelConfigurationDialog.Designer.cs

@@ -313,7 +313,7 @@ internal T OpenAndParseConfigurationFile<T>() where T : ProbeGroup
 
             if (ofd.ShowDialog() == DialogResult.OK && File.Exists(ofd.FileName))
             {
-                var newConfiguration = DesignHelper.DeserializeString<T>(File.ReadAllText(ofd.FileName));
+                var newConfiguration = JsonHelper.DeserializeString<T>(File.ReadAllText(ofd.FileName));
 
                 return newConfiguration;
             }
@@ -927,7 +927,7 @@ private void MenuItemSaveFile(object sender, EventArgs e)
 
             if (sfd.ShowDialog() == DialogResult.OK)
             {
-                DesignHelper.SerializeObject(ProbeGroup, sfd.FileName);
+                JsonHelper.SerializeObject(ProbeGroup, sfd.FileName);
             }
         }
 

OpenEphys.Onix1.Design/ChannelConfigurationDialog.cs

@@ -10,57 +10,6 @@ namespace OpenEphys.Onix1.Design
 {
     static class DesignHelper
     {
-        /// <summary>
-        /// Given a string with a valid JSON structure, deserialize the string to the given type.
-        /// </summary>
-        /// <typeparam name="T"></typeparam>
-        /// <param name="jsonString"></param>
-        /// <returns></returns>
-        #nullable enable
-        public static T? DeserializeString<T>(string jsonString)
-        {
-            var errors = new List<string>();
-
-            var serializerSettings = new JsonSerializerSettings()
-            {
-                Error = delegate(object sender, Newtonsoft.Json.Serialization.ErrorEventArgs args)
-                {
-                    errors.Add(args.ErrorContext.Error.Message);
-                    args.ErrorContext.Handled = true;
-                }
-            };
-
-            var obj = JsonConvert.DeserializeObject<T>(jsonString, serializerSettings);
-
-            if (errors.Count > 0)
-            {
-                MessageBox.Show($"There were errors encountered while parsing a JSON string. Check the console " +
-                    $"for an error log.", "JSON Parse Error");
-
-                foreach (var e in errors)
-                {
-                    Console.Error.WriteLine(e);
-                }
-
-                return default;
-            }
-
-            return obj;
-        }
-        #nullable disable
-
-        public static void SerializeObject(object _object, string filepath)
-        {
-            var serializerSettings = new JsonSerializerSettings()
-            {
-                NullValueHandling = NullValueHandling.Ignore,
-            };
-
-            var stringJson = JsonConvert.SerializeObject(_object, Formatting.Indented, serializerSettings);
-
-            File.WriteAllText(filepath, stringJson);
-        }
-
         public static IEnumerable<Control> GetAllControls(this Control root)
         {
             var stack = new Stack<Control>();

OpenEphys.Onix1.Design/DesignHelper.cs

@@ -37,7 +37,7 @@ public NeuropixelsV1ChannelConfigurationDialog(NeuropixelsV1ProbeConfiguration p
 
             ReferenceContacts.AddRange(ReferenceContactsList);
 
-            ProbeConfiguration = probeConfiguration;
+            ProbeConfiguration = new(probeConfiguration);
 
             HighlightEnabledContacts();
             UpdateContactLabels();
@@ -52,7 +52,7 @@ internal override ProbeGroup DefaultChannelLayout()
 
         internal override void LoadDefaultChannelLayout()
         {
-            ProbeConfiguration = new(ProbeConfiguration.SpikeAmplifierGain, ProbeConfiguration.LfpAmplifierGain, ProbeConfiguration.Reference, ProbeConfiguration.SpikeFilter);
+            ProbeConfiguration.ProbeGroup = new();
             ProbeGroup = ProbeConfiguration.ProbeGroup;
 
             OnFileOpenHandler();
@@ -62,8 +62,7 @@ internal override bool OpenFile<T>()
         {
             if (base.OpenFile<NeuropixelsV1eProbeGroup>())
             {
-                ProbeConfiguration = new((NeuropixelsV1eProbeGroup)ProbeGroup, ProbeConfiguration.SpikeAmplifierGain, ProbeConfiguration.LfpAmplifierGain, ProbeConfiguration.Reference, ProbeConfiguration.SpikeFilter);
-                ProbeGroup = ProbeConfiguration.ProbeGroup;
+                ProbeConfiguration.ProbeGroup = (NeuropixelsV1eProbeGroup)ProbeGroup;
 
                 OnFileOpenHandler();
 
@@ -112,7 +111,7 @@ internal override void DrawScale()
 
         internal override void HighlightEnabledContacts()
         {
-            if (ProbeConfiguration == null || ProbeConfiguration.ChannelMap == null)
+            if (ProbeConfiguration == null)
                 return;
 
             var contactObjects = zedGraphChannels.GraphPane.GraphObjList.OfType<BoxObj>()
@@ -125,11 +124,13 @@ internal override void HighlightEnabledContacts()
                 contact.Fill.Color = DisabledContactFill;
             }
 
+            var channelMap = ProbeConfiguration.ChannelMap;
+
             var contactsToEnable = contactObjects.Where(c =>
             {
                 var tag = c.Tag as ContactTag;
                 var channel = NeuropixelsV1Electrode.GetChannelNumber(tag.ContactIndex);
-                return ProbeConfiguration.ChannelMap[channel].Index == tag.ContactIndex;
+                return channelMap[channel].Index == tag.ContactIndex;
             });
 
             foreach (var contact in contactsToEnable)
@@ -155,11 +156,13 @@ internal override void UpdateContactLabels()
                 textObj.FontSpec.FontColor = DisabledContactTextColor;
             }
 
+            var channelMap = ProbeConfiguration.ChannelMap;
+
             textObjsToUpdate = textObjs.Where(c =>
             {
                 var tag = c.Tag as ContactTag;
                 var channel = NeuropixelsV1Electrode.GetChannelNumber(tag.ContactIndex);
-                return ProbeConfiguration.ChannelMap[channel].Index == tag.ContactIndex;
+                return channelMap[channel].Index == tag.ContactIndex;
             });
 
             foreach (var textObj in textObjsToUpdate)

OpenEphys.Onix1.Design/NeuropixelsV1ChannelConfigurationDialog.cs

@@ -8,12 +8,13 @@ namespace OpenEphys.Onix1.Design
     /// </summary>
     public partial class NeuropixelsV1Dialog : Form
     {
-        readonly NeuropixelsV1ProbeConfigurationDialog ProbeConfigurationDialog;
+        internal readonly NeuropixelsV1ProbeConfigurationDialog ProbeConfigurationDialog;
 
         /// <summary>
         /// Public <see cref="IConfigureNeuropixelsV1"/> interface that is manipulated by
         /// <see cref="NeuropixelsV1Dialog"/>.
         /// </summary>
+        [Obsolete]
         public IConfigureNeuropixelsV1 ConfigureNode { get; set; }
 
         /// <summary>
@@ -25,24 +26,10 @@ public NeuropixelsV1Dialog(IConfigureNeuropixelsV1 configureNode)
             InitializeComponent();
             Shown += FormShown;
 
-            if (configureNode is ConfigureNeuropixelsV1e configureV1e)
-            {
-                ConfigureNode = new ConfigureNeuropixelsV1e(configureV1e);
-            }
-            else if (configureNode is ConfigureNeuropixelsV1f configureV1f)
-            {
-                ConfigureNode = new ConfigureNeuropixelsV1f(configureV1f);
-            }
-
-            ProbeConfigurationDialog = new(ConfigureNode.ProbeConfiguration, ConfigureNode.AdcCalibrationFile, ConfigureNode.GainCalibrationFile, ConfigureNode.InvertPolarity)
-            {
-                TopLevel = false,
-                FormBorderStyle = FormBorderStyle.None,
-                Dock = DockStyle.Fill,
-                Parent = this
-            };
-
-            panelProbe.Controls.Add(ProbeConfigurationDialog);
+            ProbeConfigurationDialog = new(configureNode.ProbeConfiguration);
+            ProbeConfigurationDialog
+                .SetChildFormProperties(this)
+                .AddDialogToPanel(panelProbe);
 
             this.AddMenuItemsFromDialogToFileOption(ProbeConfigurationDialog);
         }
@@ -62,19 +49,7 @@ private void FormShown(object sender, EventArgs e)
 
         internal void Okay_Click(object sender, EventArgs e)
         {
-            SaveVariables();
-
             DialogResult = DialogResult.OK;
         }
-
-        internal void SaveVariables()
-        {
-            ConfigureNode.ProbeConfiguration = ProbeConfigurationDialog.ProbeConfiguration;
-
-            ConfigureNode.GainCalibrationFile = ProbeConfigurationDialog.textBoxGainCalibrationFile.Text;
-            ConfigureNode.AdcCalibrationFile = ProbeConfigurationDialog.textBoxAdcCalibrationFile.Text;
-
-            ConfigureNode.InvertPolarity = ProbeConfigurationDialog.InvertPolarity;
-        }
     }
 }

OpenEphys.Onix1.Design/NeuropixelsV1Dialog.cs

@@ -22,11 +22,7 @@ public override bool EditComponent(ITypeDescriptorContext context, object compon
 
                     if (editorDialog.ShowDialog() == DialogResult.OK)
                     {
-                        configureNeuropixelsV1.Enable = editorDialog.ConfigureNode.Enable;
-                        configureNeuropixelsV1.GainCalibrationFile = editorDialog.ConfigureNode.GainCalibrationFile;
-                        configureNeuropixelsV1.AdcCalibrationFile = editorDialog.ConfigureNode.AdcCalibrationFile;
-                        configureNeuropixelsV1.ProbeConfiguration = editorDialog.ConfigureNode.ProbeConfiguration;
-                        configureNeuropixelsV1.InvertPolarity = editorDialog.ConfigureNode.InvertPolarity;
+                        configureNeuropixelsV1.ProbeConfiguration = editorDialog.ProbeConfigurationDialog.ProbeConfiguration;
 
                         return true;
                     }

OpenEphys.Onix1.Design/NeuropixelsV1Editor.cs

@@ -26,45 +26,36 @@ private enum ChannelPreset
         }
 
         /// <summary>
-        /// Public <see cref="IConfigureNeuropixelsV2"/> interface that is manipulated by
-        /// <see cref="NeuropixelsV2eDialog"/>.
+        /// Gets or sets the probe configuration.
         /// </summary>
-        /// <remarks>
-        /// When a <see cref="IConfigureNeuropixelsV2"/> is passed to 
-        /// <see cref="NeuropixelsV1Dialog"/>, it is copied and stored in this
-        /// variable so that any modifications made to configuration settings can be easily reversed
-        /// by not copying the new settings back to the original instance.
-        /// </remarks>
-        public NeuropixelsV1ProbeConfiguration ProbeConfiguration { get; set; }
+        public NeuropixelsV1ProbeConfiguration ProbeConfiguration
+        {
+            get => ChannelConfiguration.ProbeConfiguration;
+            set => ChannelConfiguration.ProbeConfiguration = value;
+        }
 
-        /// <inheritdoc cref="ConfigureNeuropixelsV1e.InvertPolarity"/>
-        public bool InvertPolarity { get; set; }
+        /// <inheritdoc cref="NeuropixelsV1ProbeConfiguration.InvertPolarity"/>
+        [Obsolete]
+        public bool InvertPolarity
+        {
+            get => ProbeConfiguration.InvertPolarity;
+            set => ProbeConfiguration.InvertPolarity = value;
+        }
 
         /// <summary>
         /// Initializes a new instance of <see cref="NeuropixelsV1Dialog"/>.
         /// </summary>
         /// <param name="probeConfiguration">A <see cref="NeuropixelsV1ProbeConfiguration"/> object holding the current configuration settings.</param>
-        /// <param name="adcCalibrationFile">String defining the path to the ADC calibration file.</param>
-        /// <param name="gainCalibrationFile">String defining the path to the gain calibration file.</param>
-        /// <param name="invertPolarity">Boolean denoting whether or not to invert the polarity of neural data.</param>
-        public NeuropixelsV1ProbeConfigurationDialog(NeuropixelsV1ProbeConfiguration probeConfiguration, string adcCalibrationFile, string gainCalibrationFile, bool invertPolarity)
+        public NeuropixelsV1ProbeConfigurationDialog(NeuropixelsV1ProbeConfiguration probeConfiguration)
         {
             InitializeComponent();
             Shown += FormShown;
 
-            ProbeConfiguration = new(probeConfiguration);
-
-            ChannelConfiguration = new(ProbeConfiguration)
-            {
-                TopLevel = false,
-                FormBorderStyle = FormBorderStyle.None,
-                Dock = DockStyle.Fill,
-                Parent = this,
-            };
-
-            InvertPolarity = invertPolarity;
+            ChannelConfiguration = new(probeConfiguration);
+            ChannelConfiguration
+                .SetChildFormProperties(this)
+                .AddDialogToPanel(panelProbe);
 
-            panelProbe.Controls.Add(ChannelConfiguration);
             this.AddMenuItemsFromDialogToFileOption(ChannelConfiguration);
 
             ChannelConfiguration.OnZoom += UpdateTrackBarLocation;
@@ -85,12 +76,14 @@ public NeuropixelsV1ProbeConfigurationDialog(NeuropixelsV1ProbeConfiguration pro
             checkBoxSpikeFilter.Checked = ProbeConfiguration.SpikeFilter;
             checkBoxSpikeFilter.CheckedChanged += SpikeFilterIndexChanged;
 
-            checkBoxInvertPolarity.Checked = InvertPolarity;
+            checkBoxInvertPolarity.Checked = ProbeConfiguration.InvertPolarity;
             checkBoxInvertPolarity.CheckedChanged += InvertPolarityIndexChanged;
 
-            textBoxAdcCalibrationFile.Text = adcCalibrationFile;
+            textBoxAdcCalibrationFile.Text = ProbeConfiguration.AdcCalibrationFileName;
+            textBoxAdcCalibrationFile.TextChanged += (sender, e) => ProbeConfiguration.AdcCalibrationFileName = ((TextBox)sender).Text;
 
-            textBoxGainCalibrationFile.Text = gainCalibrationFile;
+            textBoxGainCalibrationFile.Text = ProbeConfiguration.GainCalibrationFileName;
+            textBoxGainCalibrationFile.TextChanged += (sender, e) => ProbeConfiguration.GainCalibrationFileName = ((TextBox)sender).Text;
 
             comboBoxChannelPresets.DataSource = Enum.GetValues(typeof(ChannelPreset));
             CheckForExistingChannelPreset();
@@ -101,7 +94,7 @@ public NeuropixelsV1ProbeConfigurationDialog(NeuropixelsV1ProbeConfiguration pro
 
         private void InvertPolarityIndexChanged(object sender, EventArgs e)
         {
-            InvertPolarity = ((CheckBox)sender).Checked;
+            ProbeConfiguration.InvertPolarity = ((CheckBox)sender).Checked;
         }
 
         private void FormShown(object sender, EventArgs e)

OpenEphys.Onix1.Design/NeuropixelsV1ProbeConfigurationDialog.cs

@@ -43,8 +43,6 @@ public NeuropixelsV1eHeadstageDialog(ConfigureNeuropixelsV1e configureNeuropixel
 
         private void Okay_Click(object sender, System.EventArgs e)
         {
-            DialogNeuropixelsV1e.SaveVariables();
-
             DialogResult = DialogResult.OK;
         }
     }

OpenEphys.Onix1.Design/NeuropixelsV1eHeadstageDialog.cs

@@ -23,13 +23,9 @@ public override bool EditComponent(ITypeDescriptorContext context, object compon
 
                     if (editorDialog.ShowDialog() == DialogResult.OK)
                     {
-                        configureHeadstage.Bno055.Enable = ((ConfigurePolledBno055)editorDialog.DialogBno055.Device).Enable;
+                        DesignHelper.CopyProperties((ConfigurePolledBno055)editorDialog.DialogBno055.Device, configureHeadstage.Bno055, DesignHelper.PropertiesToIgnore);
 
-                        configureHeadstage.NeuropixelsV1e.AdcCalibrationFile = editorDialog.DialogNeuropixelsV1e.ConfigureNode.AdcCalibrationFile;
-                        configureHeadstage.NeuropixelsV1e.GainCalibrationFile = editorDialog.DialogNeuropixelsV1e.ConfigureNode.GainCalibrationFile;
-                        configureHeadstage.NeuropixelsV1e.Enable = editorDialog.DialogNeuropixelsV1e.ConfigureNode.Enable;
-                        configureHeadstage.NeuropixelsV1e.ProbeConfiguration = editorDialog.DialogNeuropixelsV1e.ConfigureNode.ProbeConfiguration;
-                        configureHeadstage.NeuropixelsV1e.InvertPolarity = editorDialog.DialogNeuropixelsV1e.ConfigureNode.InvertPolarity;
+                        configureHeadstage.NeuropixelsV1e.ProbeConfiguration = editorDialog.DialogNeuropixelsV1e.ProbeConfigurationDialog.ProbeConfiguration;
 
                         return true;
                     }

OpenEphys.Onix1.Design/NeuropixelsV1eHeadstageEditor.cs

@@ -61,9 +61,6 @@ public NeuropixelsV1fHeadstageDialog(ConfigureNeuropixelsV1f configureNeuropixel
 
         private void Okay_Click(object sender, System.EventArgs e)
         {
-            DialogNeuropixelsV1A.SaveVariables();
-            DialogNeuropixelsV1B.SaveVariables();
-
             DialogResult = DialogResult.OK;
         }
     }