re #27: Improvements to outgoing data structure and naming

re #25: Decoupled plotting the spectrum from classifying the spectrum re #26: Added scene initialization functions
PerkLab · Nov 15, 2022 · 931cf29 · 931cf29
1 parent 1b44681
commit 931cf29
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diff --git a/BroadbandSpecModule/BroadbandSpecModule.py b/BroadbandSpecModule/BroadbandSpecModule.py
diff --git a/BroadbandSpecModule/Resources/UI/BroadbandSpecModule.ui b/BroadbandSpecModule/Resources/UI/BroadbandSpecModule.ui
@@ -139,6 +139,19 @@
      </property>
     </widget>
    </item>
+   <item>
+    <widget class="QPushButton" name="enableClassificationButton">
+     <property name="text">
+      <string>Enable Classification</string>
+     </property>
+     <property name="checkable">
+      <bool>true</bool>
+     </property>
+     <property name="checked">
+      <bool>false</bool>
+     </property>
+    </widget>
+   </item>
    <item>
     <widget class="ctkCollapsibleButton" name="dataCollectionSection_2">
      <property name="enabled">

diff --git a/Config/PlusDeviceSet_Server_ThorLabsVideoCapture.xml b/Config/PlusDeviceSet_Server_ThorLabsVideoCapture.xml
@@ -0,0 +1,44 @@
+<PlusConfiguration version="2.0">
+
+  <DataCollection StartupDelaySec="2.0" >
+    <DeviceSet 
+      Name="PlusServer: ThorLabs spectrometer"
+      Description="Broadcasting acquired spectrum through OpenIGTLink. First image row contains wavelength value, second image row contains intensities." />
+    <Device
+      Id="VideoDevice" 
+      Type="ThorLabsVideo" >
+      <DataSources>
+        <DataSource Type="Video" Id="Video" />
+      </DataSources>      
+      <OutputChannels>
+        <OutputChannel Id="VideoStream" VideoDataSourceId="Video" />
+      </OutputChannels>
+    </Device>
+    <Device
+      Id="CaptureDevice"
+      Type="VirtualCapture"
+      BaseFilename="RecordingTest.igs.mha"
+      EnableCapturingOnStart="FALSE" >
+      <InputChannels>
+        <InputChannel Id="VideoStream" />
+      </InputChannels>
+    </Device>
+  </DataCollection>
+
+  <PlusOpenIGTLinkServer 
+    MaxNumberOfIgtlMessagesToSend="1" 
+    MaxTimeSpentWithProcessingMs="50" 
+    ListeningPort="18944" 
+    SendValidTransformsOnly="true" 
+    OutputChannelId="VideoStream" > 
+    <DefaultClientInfo> 
+      <MessageTypes> 
+        <Message Type="IMAGE" />
+      </MessageTypes>
+      <ImageNames>
+        <Image Name="Image" EmbeddedTransformToFrame="Image" />
+      </ImageNames>
+    </DefaultClientInfo>
+  </PlusOpenIGTLinkServer>
+
+</PlusConfiguration>
diff --git a/Config/ThorLabsAscension.xml b/Config/ThorLabsAscension.xml
@@ -9,8 +9,9 @@
       Type="ThorLabsVideo"
 	  AcquisitionRate="100"
 	  IntegrationTimeSec="0.1"
+	  AveragedItemsForFiltering="1"
 	  Zebra = "1"
-	  > <!-- IntegrationTimeSec default="0.05" --> <!-- AcquisitionRate Default="30" -->
+	  > <!-- IntegrationTimeSec default="0.05" --> <!-- AcquisitionRate Default="30" --> <!--  AveragedItemsForFiltering Default="20"-->
       <DataSources>
         <DataSource 
 		   Type="Video" 

diff --git a/SOP_SkinDataCollection/Pathology pictorial documentation v2.pdf b/SOP_SkinDataCollection/Pathology pictorial documentation v2.pdf
diff --git a/SOP_SkinDataCollection/SOP_v1_SpectroscopeSkinDataCollection.docx b/SOP_SkinDataCollection/SOP_v1_SpectroscopeSkinDataCollection.docx
diff --git a/SOP_SkinDataCollection/SkinDataSetup.jpeg b/SOP_SkinDataCollection/SkinDataSetup.jpeg
diff --git a/SavedScenes/Sequence_pseudoSpectrum.seq.nrrd b/SavedScenes/Sequence_pseudoSpectrum.seq.nrrd
diff --git a/TrainedModels/Old/KNN_BlueVsWhite.joblib b/TrainedModels/Old/KNN_BlueVsWhite.joblib
diff --git a/TrainedModels/Old/KNN_CardboardVsTeaBox.joblib b/TrainedModels/Old/KNN_CardboardVsTeaBox.joblib
diff --git a/TrainedModels/Old/KNN_TestModel.joblib b/TrainedModels/Old/KNN_TestModel.joblib
diff --git a/TrainedModels/Old/my_checkpoint.pth.tar b/TrainedModels/Old/my_checkpoint.pth.tar
diff --git a/fullPipelineImplementation_Archive.ipynb → v1_881_Data2Model_Testing.ipynb b/fullPipelineImplementation_Archive.ipynb → v1_881_Data2Model_Testing.ipynb
diff --git a/fullPipelineImplementation - Copy.ipynb → v2_fullPipelineImplementation.ipynb b/fullPipelineImplementation - Copy.ipynb → v2_fullPipelineImplementation.ipynb
diff --git a/fullPipelineImplementation.ipynb → v3_fullPipelineImplementation.ipynb b/fullPipelineImplementation.ipynb → v3_fullPipelineImplementation.ipynb
diff --git a/v4_Data2Model.ipynb b/v4_Data2Model.ipynb