Merge pull request #121 from enkaoua/master

BARD fixes

config/example_config.json

@@ -25,7 +25,7 @@
     "models": {
         "models_dir": "data/models",
 	"target_model_vertices": [-1],
-	"model_visibilities": [1],
+	"model_visibilities": [0],
 	"model_opacities": [0.5, 1.0, 1.0],
 	"model_representations": ["w", "s", "s"],
         "reference_to_model": "data/reference_to_model.txt",

config/pointer_markers.json

@@ -0,0 +1,30 @@
+{
+    "camera": {
+        "source": 0,
+        "window size": [640, 480],
+        "calibration directory": "data/calibration/matts_mbp_640_x_480"
+    },
+    "tracker": {
+	    "type" : "sksaruco",
+	    "source" : 0,
+	    "calibration directory": "data/calibration/matts_mbp_640_x_480",
+
+	    "rigid bodies" : [
+		    {
+			    "name" : "modelreference",
+		    	    "filename" : "data/reference.txt",
+		            "aruco dictionary" : "DICT_ARUCO_ORIGINAL"
+		    },
+		    {
+			    "name" : "pointerref",
+			    "filename" : "data/pointer.txt",
+		            "aruco dictionary" : "DICT_ARUCO_ORIGINAL"
+    		    }
+	    ]
+	},
+
+  "interaction": {
+      "keyboard": true
+  },
+	"out path" : "pointer_positions",
+}

config/reference_with_model.json

@@ -2,14 +2,18 @@
     "camera": {
         "source": 0,
         "window size": [640, 480],
-        "calibration directory": "data/calibration/matts_mbp_640_x_480"
+        "calibration directory": "data/calibration/matts_mbp_640_x_480",
+        "roi": [0, 0, 640, 480]
+
     },
     "tracker": {
 	    "type" : "sksaruco",
+	    "source" : 0,
+	    "calibration directory": "data/calibration/matts_mbp_640_x_480",
 	    "rigid bodies" : [
 		    { 
 			    "name" : "modelreference",
-		    	    "filename" : "data/reference_for_small_liver.txt",
+		    	    "filename" : "data/reference.txt",
 		            "aruco dictionary" : "DICT_ARUCO_ORIGINAL" 
 		    }
 	    ]

doc/02_0_Build_Your_Own_Systems.rst

@@ -35,6 +35,12 @@ You may need to add
 
 if you don't have administrative permissions.
 
+You may also need to install `visioneer` 
+
+::
+
+  pip install versioneer
+
 **Another method to get BARD and all its dependant packages is the following**
 ::
 

doc/02_1_Calibrate_Your_Camera.rst

@@ -55,7 +55,7 @@ Use the '-o' option to specify a directory to save to, the
 For example:
 ::
 
-  python bardVideoCalibration.py -c config/video_calib_chessboard.json -s tests/output -p myresults
+  python bardVideoCalibration.py -c config/video_calib_chessboard.json -s 0 -o tests/output -p myresults
   #usage: bardVideoCalibration.py [-h] -c CONFIG [-s SOURCE] [-o OUTPUT] [-p PREFIX] [-ni] [-v]
 
 Then, each time the program recalibrates, the results will be saved to the 'tests/output' folder, with the filename prefix 'myresults'.

doc/02_2_Tracking_With_AuRcoTags.rst

@@ -18,7 +18,7 @@ OpenCV.
    python sksurgerybard.py --config config/example_config.json
 
 
-When you place the reference marker (data/reference.pdf) in front of the webcam you should
+When you place the reference marker found in (data/resources.pdf) in front of the webcam you should
 see the tag pattern overlaid with spherical markers. Check that the webcam width and height 
 specified in the configuration file are the same as the images you performed calibration on.
 

doc/02_3_Make_Your_Own_Pointer.rst

@@ -20,9 +20,7 @@ pelvis phantom.
 ::
 
   ls data/PelvisPhantom
-  CT_Fiduicial_Markers.txt  
-  FullPelvis.vtk  
-  PhantomCroppedJuly08.gipl.gz 
+  >> CT_Fiduicial_Markers.txt  FullPelvis.vtk  PhantomCroppedJuly08.gipl.gz 
 
 For now, have a look in the file "CT_Fiduicial_Markers.txt". This is an ordered list 
 of the positions of 4 fiducial markers that we
@@ -45,17 +43,25 @@ BARD is tracking the markers, so we know where they are, however we're going to
 tip of the pointer to locate the fiducial markers. We find the tip of the pointer 
 using a "pivot calibration". The tip of the pointer is held stationary whilst the 
 markers are pivoted around the tip. Pressing the "d" key whilst BARD is running will write 
-the pointer tracking matrix to the directory pointer_positions/bard_pointer_matrices. Do this around 100
-times whilst pivoting the pointer. Whilst doing this it is important that you do not 
+the pointer tracking matrix to the directory specified in the config file pointer_markers.json, under the parameter "out path" and then inside the directory bard_pointer_matrices, so for example if the full path is specified to be pointer_positions, the pointer positions will go under the folder pointer_positions/bard_pointer_matrices.
+Obtain around 100 pointer positions by pressing the key "d" whilst pivoting the pointer. Whilst doing this, it is important that you do not 
 move either the pointer tip or the tracking system (webcam).
 
 When you have a directory of pointer matrices you can run this;
 ::
 
-  python bardPivotCalibration.py --help
   python bardPivotCalibration.py --input pointer_positions/bard_pointer_matrices
 
-The output of this should be list of 7 numbers. The first three are the x, y and z coordinates of the
+
+The output of this should be list of 7 numbers, something like this:
+
+::
+
+  Pointer Offset =  [[-100.19828771    7.16207486    4.48010691]]
+  Pivot Location =  [[-47.31630508  93.11369119 293.46139526]]
+  Residual Error =  8.382949342574744
+
+The first three are the x, y and z coordinates of the
 pointer tip relative to the tracking markers and should be copied into a file named 
 pointer_tip.txt. The next three numbers are the x,y, and z coordinates of the pointer 
 pivot point relative to the webcam. These can be ignored for now. 
@@ -67,7 +73,7 @@ less pointer poses.
 Now edit config/pointer_markers.json to include the the pointer_tag_to_tip transform, within the pointerData entry:
 ::
 
-    "pointerData": {
+    "pointer": {
         "pointer_tag_file": "data/pointer.txt",
         "pointer_tag_to_tip": "data/pointer_tip.txt"
     },

doc/02_4_Register_And_Ovelay.rst

@@ -6,12 +6,23 @@
 Register and Overlay Model
 =============================
 
-Create a plain text-file containing the coordinates of the prostate phantom fiducials, in the same order and format as data/PelvisPhantom/CT_Fiduicial_Markers.txt. These markers have been labeled on the phantom. You must measure the points using the tracked pointer, in the same order. You should end up with a file, of the same format as CT.txt, containing the corresponding world coordinates, lets call it world.txt.
+Create a plain text-file containing the coordinates of the prostate phantom fiducials, in the same order and format as data/PelvisPhantom/CT_Fiduicial_Markers.txt. 
+
+You can do this by running 
+
+::
+
+  python sksurgerybard.py --config config/pointer_markers.json
+
+These markers have been labeled on the phantom. You must measure the points using the tracked pointer, in the same order. To do this, you can place the pointer tip at each fiducial and press "d" to record the position.
+
+This should output the files into whatever output file you specified. These points can now be copied and pasted into the world.txt file
+You should end up with a file, of the same format as CT_Fiduicial_Markers.txt, containing the corresponding world coordinates, lets call it world.txt.
 
 Compute the registration of CT points in CT_Fiduicial_Markers.txt to your world points, run this;
 ::
 
-  python bardProcrustes.py -f world.txt -m data/PelvisPhantom/CT_Fiduicial_Markers.txt
+  python bardProcrustes.py -f data/PelvisPhantom/world.txt -m data/PelvisPhantom/CT_Fiduicial_Markers.txt
 
 So here -f stands for "fixed" points, also called "target" points in the literature, and -m stands for "moving" points, also called "source" points in the literature.
 This will output a rotation, a translation, and Fiducial Registration Error.