From f8b8c8662ca88497fe7642323d1787944c13f82b Mon Sep 17 00:00:00 2001 From: Matthijs van Eede Date: Wed, 22 Apr 2015 12:27:43 -0400 Subject: [PATCH 1/7] added the vtk_meshconvert script to convert between obj, stl and vtk formats --- .gitmodules | 3 +++ minc-scripts-jscholz | 1 + setup.py | 3 ++- 3 files changed, 6 insertions(+), 1 deletion(-) create mode 100644 .gitmodules create mode 160000 minc-scripts-jscholz diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000..47f22c0 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "minc-scripts-jscholz"] + path = minc-scripts-jscholz + url = https://github.com/jan-scholz/minc-scripts.git diff --git a/minc-scripts-jscholz b/minc-scripts-jscholz new file mode 160000 index 0000000..8a87e19 --- /dev/null +++ b/minc-scripts-jscholz @@ -0,0 +1 @@ +Subproject commit 8a87e1962d1cae06d94589cf9ed36872c0c1f3ee diff --git a/setup.py b/setup.py index 844aa9f..f0f9b73 100644 --- a/setup.py +++ b/setup.py @@ -23,7 +23,8 @@ "python/volumes_from_labels_only", "python/voxel_vote", "python/replace_label_with_nearest_valid_label", - "python/rotational_minctracc.py"], + "python/rotational_minctracc.py", + "minc-scripts-jscholz/vtk_meshconvert.py"], cmdclass = {'build_ext': build_ext}, ext_modules = [Extension("cython_functions", ["python/cython_functions.pyx"], include_dirs=[numpy.get_include()])] ) From d7855482b2a40393f2b56678c7839016b13eb670 Mon Sep 17 00:00:00 2001 From: Matthijs van Eede Date: Wed, 22 Apr 2015 12:40:13 -0400 Subject: [PATCH 2/7] added info on how to clone the repository making sure that the submodules are downloaded as well --- README => README.md | 8 ++++++++ 1 file changed, 8 insertions(+) rename README => README.md (83%) diff --git a/README b/README.md similarity index 83% rename from README rename to README.md index 8f719c9..915e133 100644 --- a/README +++ b/README.md @@ -3,6 +3,14 @@ minc-stuffs is repository that houses scripts and bits of code that are useful f This code is licensed under the 3-clause BSD License. http://opensource.org/licenses/BSD-3-Clause +Installing from github: +----------------------- +`git clone --recursive https://github.com/Mouse-Imaging-Centre/minc-stuffs.git` +or +`git clone https://github.com/Mouse-Imaging-Centre/minc-stuffs.git +cd minc-stuffs +git submodule update --init --recursive` + To build and install the perl and src code: ------------------------------------------ ./autogen.sh From e1b3075d43de8a5fdac997be1c4c059b88e17f2a Mon Sep 17 00:00:00 2001 From: Matthijs van Eede Date: Wed, 22 Apr 2015 12:42:23 -0400 Subject: [PATCH 3/7] updated README --- README.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 915e133..4e63556 100644 --- a/README.md +++ b/README.md @@ -5,11 +5,15 @@ http://opensource.org/licenses/BSD-3-Clause Installing from github: ----------------------- -`git clone --recursive https://github.com/Mouse-Imaging-Centre/minc-stuffs.git` +

+git clone --recursive https://github.com/Mouse-Imaging-Centre/minc-stuffs.git
+<\pre><\code>
 or
-`git clone https://github.com/Mouse-Imaging-Centre/minc-stuffs.git
+

+git clone https://github.com/Mouse-Imaging-Centre/minc-stuffs.git
 cd minc-stuffs
-git submodule update --init --recursive`
+git submodule update --init --recursive
+<\pre><\code>
 
 To build and install the perl and src code:
 ------------------------------------------

From 3b43ec0fd2b1126085b523e0b776318bcd02c36b Mon Sep 17 00:00:00 2001
From: Matthijs van Eede 
Date: Wed, 22 Apr 2015 12:43:32 -0400
Subject: [PATCH 4/7] updated README (fixed wrong slash)

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 4e63556..20a0773 100644
--- a/README.md
+++ b/README.md
@@ -7,13 +7,13 @@ Installing from github:
 -----------------------
 

 git clone --recursive https://github.com/Mouse-Imaging-Centre/minc-stuffs.git
-<\pre><\code>
+

 or
 

 git clone https://github.com/Mouse-Imaging-Centre/minc-stuffs.git
 cd minc-stuffs
 git submodule update --init --recursive
-<\pre><\code>
+

 
 To build and install the perl and src code:
 ------------------------------------------

From 763beffc4321cea11d2cbd8c77b135131ddcd9bb Mon Sep 17 00:00:00 2001
From: Matthijs van Eede 
Date: Wed, 22 Apr 2015 14:32:25 -0400
Subject: [PATCH 5/7] updated README in terms of requirements

---
 README.md | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/README.md b/README.md
index 20a0773..7007b69 100644
--- a/README.md
+++ b/README.md
@@ -3,6 +3,13 @@ minc-stuffs is repository that houses scripts and bits of code that are useful f
 This code is licensed under the 3-clause BSD License. 
 http://opensource.org/licenses/BSD-3-Clause
 
+Prerequisites:
+--------------
+In order to run vtk_meshconvert.py you need to have VTK installed. This can be done using (April 2015):
+

+sudo apt-get install libvtk5-dev python-vtk
+

+
 Installing from github:
 -----------------------
 


From 4e56b842c42c097a45c4beb4e5a2c57295d48ccc Mon Sep 17 00:00:00 2001
From: Matthijs van Eede 
Date: Wed, 22 Apr 2015 14:34:55 -0400
Subject: [PATCH 6/7] updated NEWS, bumped version to 0.1.7

---
 NEWS     | 4 ++++
 setup.py | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/NEWS b/NEWS
index 53267f0..576fa3c 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,7 @@
+New in Version 0.1.7
+====================
+* added vtk_meshconvert.py a program that can be used to convert between BIC obj, stl and vtk meshes
+
 New in Version 0.1.6
 ====================
 * fixes egg-info file issues. The minc-stuffs version information will be produced correctly now
diff --git a/setup.py b/setup.py
index f0f9b73..74c8b38 100644
--- a/setup.py
+++ b/setup.py
@@ -13,7 +13,7 @@
     m.Extension.__dict__ = m._Extension.__dict__
 
 setup(name="python-stuffs",
-      version='0.1.6',
+      version='0.1.7',
       scripts=["python/TFCE",
                "python/smooth_vector",
                "python/measure_xcorr",

From fc97865136aef7acca97552481366e510ec18a4b Mon Sep 17 00:00:00 2001
From: Matthijs van Eede 
Date: Wed, 22 Apr 2015 14:36:10 -0400
Subject: [PATCH 7/7] updated NEWS

---
 NEWS | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS b/NEWS
index 576fa3c..098e9fa 100644
--- a/NEWS
+++ b/NEWS
@@ -1,6 +1,7 @@
 New in Version 0.1.7
 ====================
 * added vtk_meshconvert.py a program that can be used to convert between BIC obj, stl and vtk meshes
+* added bayes_intensity_update a program that updates an image based on prior knowledge coming from a population (and its stdev)
 
 New in Version 0.1.6
 ====================