solves ERROR: Unexpected indentation for sphinx-build (#115)

doc/02_0_Build_Your_Own_Systems.rst

@@ -17,43 +17,51 @@ Build Your Own Image Guided Surgery System
 
 3. Get B.A.R.D.
 ::
+
   git clone https://github.com/SciKit-Surgery/scikit-surgerybard.git
 
 or navigate to https://github.com/SciKit-Surgery/scikit-surgerybard
 and use the download button
 
 navigate to the scikit-surgerybard directory and run
 ::
+
   pip install .
 
 You may need to add
 ::
+
   pip install --user
 
 if you don't have administrative permissions.
 
 **Another method to get BARD and all its dependant packages is the following**
 ::
+
   git clone https://github.com/SciKit-Surgery/scikit-surgerybard.git
 
 Change directory to the newly created `scikit-surgerybard` by
 ::
+
   cd scikit-surgerybard
 
 Run the tox commands
 ::
+
   tox
 
 If tox run successfully,
 For Mac and Linux, activate the virtual environment using command
 ::
+
   source .tox/py36/bin/activate
 
 If all goes well the prompt should be preceded by (py36).
 
 
 For Windows, activate the virtual environment using command
 ::
+
   .tox\py36\Scripts\activate
 
 If all goes well the prompt should be preceded by (py36).

doc/02_1_Calibrate_Your_Camera.rst

@@ -30,6 +30,7 @@ or write a script to make one.
 
 Take 5-20 pictures of chessboard using:
 ::
+
   python bardVideoCalibration.py -c config/video_calib_chessboard.json
 
 Hit the 'c' key to capture an image. Press the 'q' key to quite the application.
@@ -53,6 +54,7 @@ Use the '-s' option to specify a directory to save to, and the
 
 For example:
 ::
+
   python bardVideoCalibration.py -c config/video_calib_chessboard.json -s tests/output -p myresults
 
 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

@@ -14,6 +14,7 @@ OpenCV.
 
 1. Try running the following, and check that the USB camera can track the reference marker
 ::
+
    python sksurgerybard.py --config config/example_config.json
 
 
@@ -36,7 +37,8 @@ a registration to be performed once. Here we have glued the marker to the phanto
 so model2reference should not change.
 
 Now try running
-:: 
+::
+
    python sksurgerybard.py --config config/reference_with_model.json
 
 Move the webcam so that the reference markers are visible, and you should see

doc/02_3_Make_Your_Own_Pointer.rst

@@ -18,6 +18,7 @@ can be reliably located in both the model (e.g. CT scan) and patient (i.e. physi
 Within the data directory there are files based on a CT scan of the
 pelvis phantom. 
 ::
+
   ls data/PelvisPhantom
   CT_Fiduicial_Markers.txt  
   FullPelvis.vtk  
@@ -36,6 +37,7 @@ pointer, using the "pointer" markers, a pen, some cardboard and some sort of adh
 
 Now run this:
 ::
+
   python sksurgerybard.py --config config/pointer_markers.json
 
 Move the pointer around in front of the camera. You should be able to see that 
@@ -49,6 +51,7 @@ 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
 
@@ -63,13 +66,15 @@ less pointer poses.
 
 Now edit config/pointer_markers.json to include the the pointer_tag_to_tip transform, within the pointerData entry:
 ::
+
     "pointerData": {
         "pointer_tag_file": "data/pointer.txt",
         "pointer_tag_to_tip": "data/pointer_tip.txt"
     },
 
 Now run; 
 ::
+
   python sksurgerybard.py --config config/pointer_markers.json
 
 When you place the pointer in front of the camera, you should now see an additional sphere

doc/02_4_Register_And_Ovelay.rst

@@ -10,12 +10,14 @@ Create a plain text-file containing the coordinates of the prostate phantom fidu
 
 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
 
 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.
 Cut and paste the rotation and translation into a CT_to_world.txt file as 
 ::
+
   R11 R12 R13 T1
   R21 R22 R23 T2
   R31 R31 R33 T3
@@ -25,6 +27,7 @@ and edit config/reference_with_model.json to use this file instead of data/id.tx
 
 Rerun BARD using this configuration file, using:
 ::
+
    python sksurgerybard.py --config config/reference_with_model.json
 
 and see what happens.