Merge pull request #29 in CURV/stereo-needle-localization from dev to master

* commit '0fddde19ccd1aa55b0d7df2dcc4dccf7e1ff5142': (53 commits)
  Randomize offset magnitude
  Parameterized offset magnitude in config
  Shift target in random direction when k is pressed
  Among other things, reduced noise in tip orientation measurement and plot associated axes at tip
  Use live phantom pose for refraction compensation
  Updated camera calibration. Draw reprojected points for target.
  Draw reprojected tip position. Offset ROI to left of tip.
  Reduced ROI size
  Parameterized deque length
  Parameterized upper threshold for motion
  Lowered upper bound for motion magnitude
  Use average motion by comparing current frame to several prior frames
  Temp disabled phantom markers
  Draw mask from corners
  Calcuate phantom corner vertex positions in camera images
  Added class to track phantom board in live video
  Ignore retraction segmentation, revise leftwards angle
  Fix incorrect multiplication by degrees instead of radians
  Rescale DOF HSV back to visible range
  Recalibrated camera transforms
  ...

Author: Joseph Schornak

config.xml

@@ -2,16 +2,18 @@
 <data>
 	<ip>192.168.0.100</ip>
 	<port>18944</port>
-	<output_dir>./data/</output_dir>
-	<prefix>alignment_test</prefix>
-	<!--<prefix>optitrack</prefix>-->
+
+	<output_dir>./data/Trial12 TargetShift/</output_dir>
+	<prefix>insertion</prefix>
 	<calibration_file>calibration.npz</calibration_file>
 
 	<index_camera_top>1</index_camera_top>
 	<index_camera_side>2</index_camera_side>
 	<index_camera_aux>3</index_camera_aux>
 
-	<hue_motion>110</hue_motion>
+	<frame_deque_size>3</frame_deque_size>
+
+	<hue_motion>135</hue_motion>
 	<hue_motion_range>20</hue_motion_range>
 
 	<hue_target_min>40</hue_target_min>
@@ -25,14 +27,18 @@
 	<camera_top_contrast>200</camera_top_contrast>
 	<camera_top_brightness>180</camera_top_brightness>
 
-	<camera_side_focus_absolute>50</camera_side_focus_absolute>
+	<camera_side_focus_absolute>60</camera_side_focus_absolute>
 	<camera_side_contrast>200</camera_side_contrast>
 	<camera_side_brightness>180</camera_side_brightness>
 
+	<roi_width>150</roi_width>
+	<roi_height>50</roi_height>
+
 	<kernel_top>5</kernel_top>
 	<kernel_side>5</kernel_side>
 
-	<threshold_mag>3</threshold_mag>
+	<threshold_mag_lower>2</threshold_mag_lower>
+	<threshold_mag_upper>15</threshold_mag_upper>
 
 	<dof_top>
 		<pyr_scale>0.5</pyr_scale>
@@ -53,4 +59,6 @@
 
 	<index_refraction_phantom>1.5</index_refraction_phantom>
 	<index_refraction_ambient>1.0</index_refraction_ambient>
+
+	<target_shift_magnitude>0.005</target_shift_magnitude>
 </data>

ir_registration_offset.py

@@ -4,17 +4,17 @@ camera_name: narrow_stereo/left
 camera_matrix:
   rows: 3
   cols: 3
-  data: [640.262084, 0.000000, 275.429624, 0.000000, 638.173949, 250.600262, 0.000000, 0.000000, 1.000000]
+  data: [626.236678, 0.000000, 256.530035, 0.000000, 628.651577, 268.943674, 0.000000, 0.000000, 1.000000]
 distortion_model: plumb_bob
 distortion_coefficients:
   rows: 1
   cols: 5
-  data: [0.029181, -0.069826, -0.000709, -0.014565, 0.000000]
+  data: [0.028940, -0.055310, 0.001511, -0.027066, 0.000000]
 rectification_matrix:
   rows: 3
   cols: 3
-  data: [0.999421, -0.006984, -0.033299, -0.018122, 0.719058, -0.694714, 0.028796, 0.694915, 0.718515]
+  data: [0.996103, 0.017985, -0.086347, -0.071866, 0.733062, -0.676354, 0.051134, 0.679924, 0.731498]
 projection_matrix:
   rows: 3
   cols: 4
-  data: [646.336004, 0.000000, 308.874763, 0.000000, 0.000000, 646.336004, 226.599552, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000]
+  data: [662.255268, 0.000000, 316.381474, 0.000000, 0.000000, 662.255268, 253.529610, 0.000000, 0.000000, 0.000000, 1.000000, 0.000000]