Merge pull request #81 from ofgulban/devel

Fix smoothing filter bug

.appveyor.yml

@@ -2,7 +2,7 @@ build: false
 
 environment:
   matrix:
-    - PYTHON_VERSION: 3.6
+    - PYTHON_VERSION: 3.7
       MINICONDA: C:\Miniconda
 
 init:
@@ -12,8 +12,11 @@ install:
   - "set PATH=%MINICONDA%;%MINICONDA%\\Scripts;%PATH%"
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
-  - "conda env create --force -f environment.yml python=3.6"
+  - conda config --add channels conda-forge
+  - conda info -a
+  - "conda env create -q -n segmentator python=%PYTHON_VERSION% --file requirements.txt"
   - activate segmentator
+  - pip install compoda
   - python setup.py install
 
 test_script:

.coveragerc

@@ -7,3 +7,5 @@ omit =
     *config*
     *tests/*
     segmentator/future/*
+    segmentator/cython/*
+    *ui.py

README.md

@@ -1,4 +1,4 @@
-[![DOI](https://zenodo.org/badge/59303623.svg)](https://zenodo.org/badge/latestdoi/59303623) [![Build Status](https://travis-ci.org/ofgulban/segmentator.svg?branch=master)](https://travis-ci.org/ofgulban/segmentator) [![Build status](https://ci.appveyor.com/api/projects/status/lkxp4y5ahssqv6ng?svg=true)](https://ci.appveyor.com/project/ofgulban/segmentator) [![codecov](https://codecov.io/gh/ofgulban/segmentator/branch/master/graph/badge.svg)](https://codecov.io/gh/ofgulban/segmentator) [![Code Health](https://landscape.io/github/ofgulban/segmentator/master/landscape.svg?style=flat)](https://landscape.io/github/ofgulban/segmentator/master) [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/segmentator/Lobby)
+[![DOI](https://zenodo.org/badge/59303623.svg)](https://zenodo.org/badge/latestdoi/59303623) [![Build Status](https://travis-ci.org/ofgulban/segmentator.svg?branch=master)](https://travis-ci.org/ofgulban/segmentator) [![Build status](https://ci.appveyor.com/api/projects/status/lkxp4y5ahssqv6ng?svg=true)](https://ci.appveyor.com/project/ofgulban/segmentator) [![codecov](https://codecov.io/gh/ofgulban/segmentator/branch/master/graph/badge.svg)](https://codecov.io/gh/ofgulban/segmentator) [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/segmentator/Lobby)
 
 # Segmentator
 
@@ -27,7 +27,6 @@ The goal is to provide a complementary tool to the already available brain tissu
 | [Compoda](https://github.com/ofgulban/compoda) | 0.3.3          |
 
 ## Installation & Quick Start
-- Make sure you have [**pip**](https://en.wikipedia.org/wiki/Pip_(package_manager)) installed if you are using [**Python 2.7**](https://www.python.org/download/releases/2.7/).
 - Download [the latest release](https://github.com/ofgulban/segmentator/releases) and unzip it.
 - Change directory in your command line:
 ```

requirements.txt

@@ -3,4 +3,3 @@ scipy==1.0.0
 matplotlib==2.2.2
 nibabel==2.2.1
 pytest-cov==2.5.1
-compoda>=0.3

segmentator/config_filters.py

@@ -11,3 +11,4 @@
 edge_thr = 0.001
 gamma = 1
 downsampling = 0
+no_nonpositive_mask = False

segmentator/filter.py

@@ -20,7 +20,7 @@
 from __future__ import division
 import os
 import numpy as np
-import config_filters as cfg
+import segmentator.config_filters as cfg
 from nibabel import load, Nifti1Image, save
 from numpy.linalg import eigh
 from scipy.ndimage import gaussian_filter
@@ -71,7 +71,11 @@ def QC_export(image, basename, identifier, nii):
 else:
     pass
 
-idx_msk_flat = ima.flatten() != 0
+if cfg.no_nonpositive_mask:  # TODO: work in progress
+    idx_msk_flat = np.ones(ima.size, dtype=bool)
+else:  # mask out non positive voxels
+    idx_msk_flat = ima.flatten() > 0
+
 dims = ima.shape
 
 # The main loop

segmentator/filters_ui.py

@@ -73,6 +73,10 @@ def main():
         help="(!WIP!) Downsampling factor, use integers > 1. E.g. factor of 2 \
         reduces the amount of voxels 8 times."
         )
+    parser.add_argument(
+        "--no_nonpositive_mask", action='store_true',
+        help="(!WIP!) Do not mask out non-positive values."
+        )
 
     # set cfg file variables to be accessed from other scripts
     args = parser.parse_args()
@@ -85,6 +89,7 @@ def main():
     cfg.nr_iterations = args.nr_iterations
     cfg.save_every = args.save_every
     cfg.downsampling = args.downsampling
+    cfg.no_nonpositive_mask = args.no_nonpositive_mask
 
     welcome_str = 'Segmentator {}'.format(__version__)
     welcome_decor = '=' * len(welcome_str)

segmentator/utils.py

@@ -25,7 +25,6 @@
 from nibabel import load, Nifti1Image, save
 from scipy.ndimage import convolve
 from time import time
-from segmentator.deriche_prepare import Deriche_Gradient_Magnitude
 
 
 def sub2ind(array_shape, rows, cols):
@@ -304,6 +303,7 @@ def compute_gradient_magnitude(ima, method='scharr'):
         gra = np.asarray(np.gradient(ima))
         gra_mag = np.sqrt(np.sum(np.power(gra, 2.), axis=0))
     elif method.lower() == 'deriche':
+        from segmentator.deriche_prepare import Deriche_Gradient_Magnitude
         alpha = cfg.deriche_alpha
         print('    Selected alpha: {}'.format(alpha))
         ima = np.ascontiguousarray(ima, dtype=np.float32)