Merge pull request #40 from KVSlab/release-v0.3-and-refactor

Release v0.3 and minor refactoring

Author: hkjeldsberg

demo/demo_manipulate_area_inflation.py

@@ -11,7 +11,7 @@
 #       --method area --percentage -20 --region-of-interest first_line --poly-ball-size 250 250 250
 #  $ morphman-area --ifile C0002/surface/model.vtp --ofile C0002/surface/area_inflated.vtp \
 #       --method area --percentage 20 --region-of-interest first_line --poly-ball-size 250 250 250
-
+#
 # and a more detailed explenation could be found here:
 # https://morphman.readthedocs.io/en/latest/manipulate_area.html#inflation-deflation-of-an-arterial-segment
 

demo/get_test_data.py

@@ -12,27 +12,27 @@
 def download_case(case):
     abs_path = path.dirname(path.abspath(__file__))
     output_file = path.join(abs_path, "{}_models.tar.gz".format(case))
-    adress = "http://ecm2.mathcs.emory.edu/aneuriskdata/download/{}/{}_models.tar.gz".format(case, case)
+    url = "http://ecm2.mathcs.emory.edu/aneuriskdata/download/{}/{}_models.tar.gz".format(case, case)
 
     try:
         if platform == "darwin":
-            system("curl {} --output {}".format(adress, output_file))
+            system("curl {} --output {}".format(url, output_file))
             system("tar -zxvf {}".format(output_file))
             system("rm {}".format(output_file))
 
         elif platform == "linux" or platform == "linux2":
-            system("wget {}".format(adress))
+            system("wget {}".format(url))
             system("tar -zxvf {}".format(output_file))
             system("rm {}".format(output_file))
 
         elif platform == "win32":
-            system("bitsadmin /transfer download_model /download /priority high {} {}".format(adress, output_file))
+            system("bitsadmin /transfer download_model /download /priority high {} {}".format(url, output_file))
             system("tar -zxvf {}".format(output_file))
             system("del /f {}".format(output_file))
 
     except:
         raise RuntimeError("Problem downloading the testdata, please do it manually from "
-                           + adress + " and extract the compressed tarball in the"
+                           + url + " and extract the compressed tarball in the"
                            + " test folder")
 
 

docs/source/Miscellaneous.rst

@@ -82,14 +82,15 @@ For a more detailed description of the method, please see [3]_.
 
 Common
 ======
-In ``common.py`` we have collected generic functions used by multiple scripts.
-Many of the functions wrap existing vtk and vmtk functions in a more pythonic syntax.
+In the folder ``common`` we have collected utility scripts containing generic functions used by multiple scripts.
+Many of the functions wrap existing vtk and vmtk functions in a more pythonic syntax,
+collected in ``vtk_wrapper.py`` and ``vmtk_wrapper.py``, respectively.
 Instead of writing 6-7 lines of code to initiate a vtk-object, and set each parameter,
-and the input surface, one can call one function with multiple arguments instead,
-see for instance :meth:`common.threshold`.
+and the input surface, one may call one function with multiple arguments instead,
+see for instance :meth:`vtk_wrapper.vtk_compute_threshold`.
 
 In addition to wrapping vtk and vmtk functionality, there is also new methods for
-manipulating centerlines and Voronoi diagrams.
+manipulating centerlines, surface models and Voronoi diagrams, collected in their respective scripts.
 
 .. [1] Piccinelli, M., Bacigaluppi, S., Boccardi, E., Ene-Iordache, B., Remuzzi, A., Veneziani, A. and Antiga, L., 2011. Geometry of the internal carotid artery and recurrent patterns in location, orientation, and rupture status of lateral aneurysms: an image-based computational study. Neurosurgery, 68(5), pp.1270-1285.
 .. [2] Bogunović, H., Pozo, J.M., Cárdenes, R., Villa-Uriol, M.C., Blanc, R., Piotin, M. and Frangi, A.F., 2012. Automated landmarking and geometric characterization of the carotid siphon. Medical image analysis, 16(4), pp.889-903.

docs/source/conf.py

@@ -66,9 +66,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'0.2'
+version = u'0.3'
 # The full version, including alpha/beta/rc tags.
-release = u'0.2'
+release = u'0.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/installation.rst

@@ -21,7 +21,7 @@ The general dependencies of morphMan are
 Basic Installation
 ==================
 We recommend that you can install morphMan through Anaconda.
-First, install Anaconda or Miniconda (preferably the python 3.6 version).
+First, install Anaconda or Miniconda (preferably the Python 3.6 version).
 Then execute the following command in a terminal window::
 
   $ conda create -n your_environment -c vmtk -c morphman morphman

docs/source/manipulate_area.rst

@@ -9,7 +9,7 @@ Tutorial: Manipulate area
 Manipulation of the cross-sectional area is performed by running ``morphman-area`` in the terminal, followed by the
 respective command line arguments. Alternatively, you can execute the Python script directly,
 located in the ``morphman`` subfolder, by typing ``python manipulate_area.py``. We have also created a
-demo folder where we show how to run this tutorial from a Python script, please checkout the code from GitHub to
+demo folder where we show how to run this tutorial from a Python script, please check out the code from GitHub to
 run the demos.
 
 In this tutorial, we are using the model with

docs/source/manipulate_bend.rst

@@ -10,7 +10,7 @@ The goal of ``morphman-bend``, is to alter one specific bend in the
 vasculature, like shown in Figure 1. This can be performed by running ``morphman-bend`` in the terminal,
 followed by the respective command line arguments. Alternatively, you can execute the Python script directly,
 located in the ``morphman`` subfolder, by typing ``python manipulate_bend.py``. We have also created a 
-demo folder where we show how to run this tutorial from a Python script, please checkout the code from GitHub to
+demo folder where we show how to run this tutorial from a Python script, please check out the code from GitHub to
 run the demos.
 
 .. figure:: Bend_moving.png

docs/source/manipulate_bifurcation.rst

@@ -24,7 +24,7 @@ is a file `./C0005/surface/model.vtp`, relative to where you execute the command
 Performing the manipulation can be achieved by running ``morphman-bifurcation`` in the terminal, followed by the
 respective command line arguments. Alternatively, you can execute the Python script directly,
 located in the ``morphman`` subfolder, by typing ``python manipulate_bifurcation.py``. We have also created a 
-demo folder where we show how to run this tutorial from a Python script, please checkout the code from GitHub to
+demo folder where we show how to run this tutorial from a Python script, please check out the code from GitHub to
 run the demos.
 
 Shown in Figure 2 is the result of rotating the two daughter branches with both

docs/source/manipulate_branch.rst

@@ -7,13 +7,13 @@ Tutorial: Manipulate branch
 ===========================
 
 The goal of ``manipulate_branch.py`` is to manipulate a specific branch of a
-vascular model, either through pure tranlation and rotation, or by completely removing it, as depicted in Figure 1.
+vascular model, either through pure tranlsation and rotation, or by completely removing it, as depicted in Figure 1.
 In particular, we have defined a branch as any branch branching out of the longest tubular structure,
 defined by the physical length of the tube.
 The manipulation can be achieved by running ``morphman-branch`` in the terminal, followed by the
 respective command line arguments. Alternatively, you can execute the Python script directly,
 located in the ``morphman`` subfolder, by typing ``python manipulate_branch.py``. We have also created a
-demo folder where we show how to run this tutorial from a Python script, please checkout the code from GitHub to
+demo folder where we show how to run this tutorial from a Python script, please check out the code from GitHub to
 run the demos.
 
 .. figure:: Branch.png

docs/source/manipulate_curvature.rst

@@ -11,7 +11,7 @@ total curvature/torsion in a vascular segment, see Figure 1 for an example.
 The manipulation can be achieved by running ``morphman-curvature`` in the terminal, followed by the
 respective command line arguments. Alternatively, you can execute the Python script directly,
 located in the ``morphman`` subfolder, by typing ``python manipulate_curvature.py``. We have also created a 
-demo folder where we show how to run this tutorial from a Python script, please checkout the code from GitHub to
+demo folder where we show how to run this tutorial from a Python script, please check out the code from GitHub to
 run the demos.
 
 .. figure:: Curvature.png