Merge pull request #66 from KVSlab/update-vmtk

Upgrade morphMan to v.1.2

.circleci/config.yml

@@ -7,7 +7,7 @@ workflows:
 jobs:
   install-and-test:
     docker:
-      - image: cimg/python:3.6
+      - image: cimg/python:3.10
     working_directory: ~/repo
     steps:
       - checkout
@@ -27,11 +27,11 @@ jobs:
             # Set conda parameters
             conda config --set restore_free_channel true
             conda config --set always_yes yes --set changeps1 no
-            conda config --add channels vmtk
+            conda config --add channels conda-forge
             conda config --add channels morphman
 
             # Set up environment
-            conda create -n morphman morphman pytest llvm=3.3
+            conda create -n morphman morphman 
 
             # Activate environment
             source activate morphman
@@ -42,11 +42,6 @@ jobs:
             # Dependencies for code coverage
             pip install pytest-cov codecov
 
-            # Edit VMTK files
-            sed -i -e 's/len(self.SourcePoints)\/3/len\(self.SourcePoints\)\/\/3/g' $HOME/miniconda/envs/morphman/lib/python3.6/site-packages/vmtk/vmtkcenterlines.py
-            sed -i -e 's/len(self.TargetPoints)\/3/len\(self.TargetPoints\)\/\/3/g' $HOME/miniconda/envs/morphman/lib/python3.6/site-packages/vmtk/vmtkcenterlines.py
-            sed -i -e 's/(len(values) - 1)\/2/\(len\(values\) - 1\)\/\/2/g' $HOME/miniconda/envs/morphman/lib/python3.6/site-packages/vmtk/vmtksurfacecurvature.py
-
             # Run tests
             cd test
             pytest --cov=./

README.md

@@ -37,7 +37,7 @@ Licence
 morphMan is licensed under the GNU GPL, version 3 or (at your option) any
 later version.
 
-morphMan is Copyright (2016-2021) by the authors.
+morphMan is Copyright (2016-2022) by the authors.
 
 Documentation
 -------------
@@ -56,7 +56,7 @@ Installation
 
 For reference, morphMan requires the following dependencies: VTK > 8.1, Numpy <= 1.13, SciPy > 1.0.0, and VMTK 1.4.
 If you are on Windows, macOS or Linux you can install all the general dependencies through anaconda.
-First install Anaconda or Miniconda (preferably the Python 3.6 version).
+First install Anaconda or Miniconda (preferably the Python 3.10 version).
 Then execute the following command
 
         conda create -n your_environment -c vmtk -c morphman morphman

appveyor.yml

@@ -17,19 +17,12 @@ environment:
     CONDA_INSTALL_LOCN: "C:\\Miniconda-x64"
 
   matrix:
-    - PYTHON: "C:\\Python35_64"
-      PYTHON_VERSION: "3.5"
+    - PYTHON: "C:\\Python39_64"
+      PYTHON_VERSION: "3.9"
       PYTHON_ARCH: "64"
-      CONDA_PY: "35"
+      CONDA_PY: "39"
       CONDA_NPY: "18"
-      APP_CONDA_PY: "3.5.1"
-
-    - PYTHON: "C:\\Python36_64"
-      PYTHON_VERSION: "3.6"
-      PYTHON_ARCH: "64"
-      CONDA_PY: "36"
-      CONDA_NPY: "18"
-      APP_CONDA_PY: "3.6.1"
+      APP_CONDA_PY: "3.9.1"
 
 platform:
   - x64
@@ -43,33 +36,21 @@ install:
   - cmd: conda config --set always_yes yes
   - cmd: conda update --quiet conda
   - cmd: conda install --quiet jinja2 conda-build=3.10.5 anaconda-client
-  - cmd: conda config --set restore_free_channel true
 
   # Add custom channels
-  - cmd: conda config --add channels vmtk
+  - cmd: conda config --add channels conda-forge
   - cmd: conda config --add channels morphman
 
-  # Install dependencies
-  - cmd: conda install pytest scipy vtk vmtk python=3.6
-
   # Set up environment
-  - cmd: conda create -n morphman_env morphman
+  - cmd: conda create -n morphman morphman pytest
 
 build: false
 
 test_script:
   # Activate environment
   - cmd: conda init cmd.exe
-  - cmd: conda activate morphman_env
-
-  # Search and replace in vmtkcenterlines.py for / to //
-  - cmd: sed -i "s/len(self.SourcePoints)\/3/len\(self.SourcePoints\)\/\/3/g" %CONDA_INSTALL_LOCN%\\Lib\\site-packages\\vmtk\\vmtkcenterlines.py
-  - cmd: sed -i "s/len(self.TargetPoints)\/3/len\(self.TargetPoints\)\/\/3/g" %CONDA_INSTALL_LOCN%\\Lib\\site-packages\\vmtk\\vmtkcenterlines.py
-  - cmd: sed -i -e "s/(len(values) - 1)\/2/\(len\(values\) - 1\)\/\/2/g" %CONDA_INSTALL_LOCN%\\Lib\\site-packages\\vmtk\\vmtksurfacecurvature.py
+  - cmd: conda activate morphman
 
   # Start testing
   - cd .\\test
-  - ps: Start-FileDownload 'http://ecm2.mathcs.emory.edu/aneuriskdata/download/C0001/C0001_models.tar.gz'
-  - tar --force-local -zxvf C0001_models.tar.gz
-  - del /f C0001_models.tar.gz
   - pytest .

conda-build/conda_build_config.yaml

@@ -1,9 +1,10 @@
 numpy:
-  - 1.13.*
+  - 1.23.*
 
 python:
-  - 3.5.1
-  - 3.6.1
+  - 3.8.*
+  - 3.9.*
+  - 3.10.*
 
 vtk:
-  - 8.1.0
+  - 9.1.*

conda-build/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: "morphman"
-  version: "1.1"
+  version: "1.2"
 
 source:
   path: ../

demo/demo_manipulate_surface.py

@@ -44,7 +44,7 @@
 default_values["poly_ball_size"] = [250, 250, 250]
 
 # Run manipulation - smooth the entire geometry except aneurysm dome
-#manipulate_surface(**default_values)
+manipulate_surface(**default_values)
 
 ### Add noise to the surface
 # Output file path

demo/get_test_data.py

@@ -5,30 +5,26 @@
 ##      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 ##      PURPOSE.  See the above copyright notices for more information.
 
-from os import system, path
+from os import system, path, makedirs
 from sys import platform
 
 
 def download_case(case):
     abs_path = path.dirname(path.abspath(__file__))
-    output_file = path.join(abs_path, "{}_models.tar.gz".format(case))
-    url = "http://ecm2.mathcs.emory.edu/aneuriskdata/download/{}/{}_models.tar.gz".format(case, case)
+    output_file = path.join(abs_path, case, "surface", "model.vtp")
+    url = "https://github.com/hkjeldsberg/AneuriskDatabase/raw/master/models/{}/surface/model.vtp".format(case)
+
+    # Create test data folders
+    if not path.exists(path.join(abs_path, case, "surface")):
+        makedirs(path.join(abs_path, case, "surface"))
 
     try:
         if platform == "darwin":
-            system("curl {} --output {}".format(url, output_file))
-            system("tar -zxvf {}".format(output_file))
-            system("rm {}".format(output_file))
-
+            system("curl -L {} --output {}".format(url, output_file))
         elif platform == "linux" or platform == "linux2":
-            system("wget {}".format(url))
-            system("tar -zxvf {}".format(output_file))
-            system("rm {}".format(output_file))
-
+            system("wget -O {} {}".format(output_file, url))
         elif platform == "win32":
             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 "

docs/source/Miscellaneous.rst

@@ -38,7 +38,7 @@ the geometric properties (curvature and torsion) of the centerline, set with
  2. Discrete derivatives (``disc``)
  3. VMTK (``vmtk``)
 
-To perform landmarking, we will be using the model with `ID C0001 <http://ecm2.mathcs.emory.edu/aneuriskdata/download/C0001/C0001_models.tar.gz>`_
+To perform landmarking, we will be using the model with `ID C0001 <https://github.com/hkjeldsberg/AneuriskDatabase/tree/master/models/C0001>`_
 from the Aneurisk database. For the commands below we assume that there is a file `./C0001/surface/model.vtp`, relative to where you execute the command.
 To landmark the surface model, run the following command::
 
@@ -71,7 +71,7 @@ manipulates only the centerline for a range of ``--alpha`` and
 ``--beta`` values. The resulting 2D data can be fitted to a surface through cubic spline interpolation, from
 which one can easily collect appropriate values for ``--alpha`` and ``--beta``.
 
-To estimate :math:`\alpha` and :math:`\beta`, we will be using the model with `ID C0005 <http://ecm2.mathcs.emory.edu/aneuriskdata/download/C0005/C0005_models.tar.gz>`_
+To estimate :math:`\alpha` and :math:`\beta`, we will be using the model with `ID C0005 <https://github.com/hkjeldsberg/AneuriskDatabase/tree/master/models/C0005>`_
 from the Aneurisk database. For the commands below we assume that there is a file `./C0005/surface/model.vtp`, relative to where you execute the command.
 
 Imagine we are interested in changing the bend angle by :math:`\pm 10^{\circ}`.

docs/source/conf.py

@@ -28,13 +28,13 @@
 # -- Project information -----------------------------------------------------
 
 project = 'morphman'
-copyright = '2021, Aslak W. Bergersen & Henrik A. Kjeldsberg'
+copyright = '2022, Aslak W. Bergersen & Henrik A. Kjeldsberg'
 author = 'Aslak W. Bergersen & Henrik A. Kjeldsberg'
 
 # The short X.Y version.
-version = '1.1'
+version = '1.2'
 # The full version, including alpha/beta/rc tags
-release = '1.1'
+release = '1.2'
 
 # -- General configuration ---------------------------------------------------
 

docs/source/installation.rst

@@ -3,6 +3,8 @@
 ============
 Installation
 ============
+.. highlight:: console
+
 morphMan (morphological manipulation) is a collection of scripts to objectively manipulate
 morphological features of patient-specific vascular geometries. The project is accessible through
 `GitHub <https://github.com/KVSlab/morphMan/>`_ and `Anaconda <https://anaconda.org/morphman/morphman>`_.
@@ -12,21 +14,24 @@ Compatibility and Dependencies
 ==============================
 The general dependencies of morphMan are 
 
-* VMTK 1.4.0
-* VTK 8.1.0
-* Numpy <= 1.13
-* SciPy 1.1.0
-* Python (2.7 or >=3.5)
+* VMTK 1.5.0
+* VTK 9.1.0
+* Numpy 1.23
+* SciPy 1.8.1
+* Python >=3.8
 
 Basic Installation
 ==================
 We recommend that you can install morphMan through Anaconda.
-First, install Anaconda or Miniconda (preferably the Python 3.6 version).
-Then execute the following command in a terminal window::
+First, install `Anaconda <https://www.anaconda.com/products/distribution>`_ or `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_.
+Then execute the following command in a terminal window to create a Conda environment with morphMan installed::
+
+  $ conda create -n your_environment -c conda-forge -c morphman morphman
 
-  $ conda create -n your_environment -c vmtk -c morphman morphman
+.. note::
+    Replace ``your_environment`` with the environment name.
 
-You can then activate your environment by running ``source activate your_environment``.
+You can then activate your environment by running ``conda activate your_environment`` or ``source activate your_environment``.
 Now you are all set, and can start using morphMan. morphMan can be accessed by opening a Python console
 and typing::
 
@@ -39,53 +44,32 @@ Alternatively you can use one of the six main methods of manipulation directly t
 
 followed by the command line arguments for the selected method. A detailed explanation for usage of morphMan is described in :ref:`getting_started`.
 
-.. WARNING:: The VMTK version 1.4, the one currently distributed with Anaconda, has a Python3 bug in `vmtkcenterlines` and `vmtksurfacecurvature`. As a workaround you have to change these files. To find out where it is located please execute::
-
-    $ which vmtkcenterlines
-    /Users/[Name]/anaconda3/envs/[your_environment]/bin/vmtkcenterlines
-    $ python -V
-    Python 3.6.2 :: Continuum Analytics, Inc.
-
-  Now copy the path up until ``[your_environment]`` and add ``lib/python3.6/site-packages/vmtk/vmtkcenterlines.py``. Please change the path separation symbol to match your operating system and change ``python3.6`` to the python version you are using. If you are using Miniconda, replace `anaconda3` with `miniconda3`. Using this path you can run the two following lines::
-
-    $ sed -i -e 's/len(self.SourcePoints)\/3/len\(self.SourcePoints\)\/\/3/g' /Users/[Name]/anaconda3/envs/[your_environment]/lib/python3.6/site-packages/vmtk/vmtkcenterlines.py
-    $ sed -i -e 's/len(self.TargetPoints)\/3/len\(self.TargetPoints\)\/\/3/g' /Users/[Name]/anaconda3/envs/[your_environment]/lib/python3.6/site-packages/vmtk/vmtkcenterlines.py
-
-  Similarly, for `vmtksurfacecurvature.py`, run the following command::
-
-    $ sed -i -e 's/(len(values) - 1)\/2/\(len\(values\) - 1\)\/\/2/g' /Users/[Name]/anaconda3/envs/[your_environment]/lib/python3.6/site-packages/vmtk/vmtksurfacecurvature.py
-
-
-.. WARNING:: Some users may experience the following Python compatibility issue::
-
-    ModuleNotFoundError: No module named 'vtkRenderingOpenGL2Python'
-
-  To fix this issue, a temporary solution is the install the ``llvm`` library directly in the virtual environment, using the following commands::
-
-    $ conda config --set restore_free_channel true
-    $ conda install llvm=3.3
-
 Development version
 ===================
 
 Downloading
 ~~~~~~~~~~~
 The latest development version of morphMan can be found on the official
 `morphMan git repository <https://github.com/KVSlab/morphMan>`_ on GitHub.
-Make sure Git (>=1.6) is installed, which is needed to clone the repository.
+Make sure `Git <https://git-scm.com/>`_ is installed, which is needed to clone the repository.
 To clone the morphMan repository, navigate to the directory where you wish
 morphMan to be stored, type the following command, and press Enter::
 
-    $ git clone https://github.com/KVSlab/morphMan
+   $ git clone https://github.com/KVSlab/morphMan
 
+If it not already present, this will install Python for you.
 After the source distribution has been downloaded, all the files required will be located
 in the newly created ``morphMan`` folder.
 
 Building
 ~~~~~~~~
 In order to build and install morphMan, navigate into the ``morphMan`` folder, where a ``setup.py``
 file will be located. First, make sure that all dependencies are installed. Then, building and installation of morphMan
-can be performed by simply running the following command from the terminal window::
+can be performed with ``pip`` by running the following command::
+
+    $ python -m pip install .
+
+Alternatively, morphMan can be installed using Python directly (deprecated)::
 
     $ python setup.py install
 

docs/source/manipulate_area.rst

@@ -13,7 +13,7 @@ demo folder where we show how to run this tutorial from a Python script, please
 run the demos.
 
 In this tutorial, we are using the model with
-`ID C0002 <http://ecm2.mathcs.emory.edu/aneuriskdata/download/C0002/C0002_models.tar.gz>`_
+`ID C0002 <https://github.com/hkjeldsberg/AneuriskDatabase/tree/master/models/C0002>`_
 from the Aneurisk database. For the commands below we assume that there is a file `./C0002/surface/model.vtp`, relative to where you execute the command.
 
 For changing the area you first need to define which segment you want to alter. For ``morphman-area`` there are

docs/source/manipulate_bend.rst

@@ -24,7 +24,7 @@ respectively. For a detailed description on how we have defined of the
 vectors :math:`\alpha` and :math:`\beta`, see [1]_.
 
 In this tutorial, we are using the model with
-`ID C0005 <http://ecm2.mathcs.emory.edu/aneuriskdata/download/C0005/C0005_models.tar.gz>`_
+`ID C0005 <https://github.com/hkjeldsberg/AneuriskDatabase/tree/master/models/C0005>`_
 from the Aneurisk database. For the commands below we assume that there is a folder
 a `./C0005/surface/model.vtp`, relative to where you execute the command.
 

docs/source/manipulate_bifurcation.rst

@@ -18,7 +18,7 @@ The algorithm builds on previous work of Ford et al. [1]_
     Figure 1: An illustration of the goal of ``morphman-bifurcation``.
 
 In this tutorial, we are using the model with
-`ID C0005 <http://ecm2.mathcs.emory.edu/aneuriskdata/download/C0005/C0005_models.tar.gz>`_
+`ID C0005 <https://github.com/hkjeldsberg/AneuriskDatabase/tree/master/models/C0005>`_
 from the Aneurisk database. For the commands below we assume that there
 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
@@ -62,7 +62,7 @@ The default is to rotate both branches, but if either ``--keep-fixed-1`` or
 fixed, respectively. Furthermore, if both parameters are set to **True**
 then the algorithm can be used to remove an aneurysm (a balloon-shaped bleb
 on the artery), see Figure 4. To this specific tutorial, we have used the model
-with `ID C0066 <http://ecm2.mathcs.emory.edu/aneuriskdata/download/C0066/C0066_models.tar.gz>`_
+with `ID C0066 <https://github.com/hkjeldsberg/AneuriskDatabase/tree/master/models/C0066>`_
 , which harbors an aneurysm located at the terminal bifurcation in the internal carotid artery.
 
 .. figure:: remove_aneurysm.png

docs/source/manipulate_branch.rst

@@ -21,7 +21,7 @@ run the demos.
   Figure 1: An illustration of the desired output from the method.
 
 In this tutorial, we are using the model with
-`ID C0002 <http://ecm2.mathcs.emory.edu/aneuriskdata/download/C0002/C0002_models.tar.gz>`_
+`ID C0002 <https://github.com/hkjeldsberg/AneuriskDatabase/tree/master/models/C0002>`_
 from the Aneurisk database. For the commands below we assume that there is a
 file `./C0002/surface/model.vtp`, relative to where you execute the command.
 

docs/source/manipulate_curvature.rst

@@ -19,7 +19,7 @@ run the demos.
   Figure 1: An illustration of the desired output from the method.
 
 In this tutorial, we are using the model with
-`ID C0005 <http://ecm2.mathcs.emory.edu/aneuriskdata/download/C0005/C0005_models.tar.gz>`_
+`ID C0005 <https://github.com/hkjeldsberg/AneuriskDatabase/tree/master/models/C0005>`_
 from the Aneurisk database. For the commands below we assume that there is a
 file `./C0005/surface/model.vtp`, relative to where you execute the command.